chr20-33788846-G-A

Variant names:

• chr20-33788846-G-A
• rs186635468
• NM_001282933.2:c.1853-17G>A

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_001282933.2(ZNF341):​c.1853-17G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00524 in 1,610,766 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0040 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0054 (22 hom.)
• Consequence: ZNF341 NM_001282933.2 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.09
• Publications: 0 publications found

Genes affected

ZNF341 (HGNC:15992): (zinc finger protein 341) Enables DNA binding activity and DNA-binding transcription activator activity. Predicted to be involved in regulation of transcription, DNA-templated. Located in nucleus. Implicated in hyper IgE recurrent infection syndrome 3. [provided by Alliance of Genome Resources, Apr 2022]

ZNF341-AS1 (HGNC:50736): (ZNF341 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 20-33788846-G-A is Benign according to our data. Variant chr20-33788846-G-A is described in ClinVar as Benign. ClinVar VariationId is 1165792.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.004 (609/152348) while in subpopulation NFE AF = 0.00628 (427/68034). AF 95% confidence interval is 0.00579. There are 1 homozygotes in GnomAd4. There are 260 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAdExome4 at 22 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001282933.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF341	NM_001282933.2	MANE Select	c.1853-17G>A		intron	N/A	NP_001269862.1	Q9BYN7-1
	ZNF341	NM_032819.5		c.1832-17G>A		intron	N/A	NP_116208.3
	ZNF341	NM_001282935.2		c.1583-17G>A		intron	N/A	NP_001269864.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF341	ENST00000375200.6	TSL:1 MANE Select	c.1853-17G>A		intron	N/A	ENSP00000364346.1	Q9BYN7-1
	ZNF341	ENST00000342427.6	TSL:1	c.1832-17G>A		intron	N/A	ENSP00000344308.2	Q9BYN7-2
	ZNF341	ENST00000483118.5	TSL:1	n.1756-17G>A		intron	N/A	ENSP00000432933.1	E9PN62

Frequencies

GnomAD3 genomes AF: 0.00400 AC: 609 AN: 152230 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.00116

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.00392

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00628

Gnomad OTH AF: 0.00239

GnomAD2 exomes AF: 0.00368 AC: 916 AN: 249236 AF XY: 0.00385

Gnomad AFR exome AF: 0.000940

Gnomad AMR exome AF: 0.00355

Gnomad ASJ exome AF: 0.00170

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00255

Gnomad NFE exome AF: 0.00592

Gnomad OTH exome AF: 0.00509

GnomAD4 exome AF: 0.00537 AC: 7826 AN: 1458418 Hom.: 22 Cov.: 30 AF XY: 0.00522 AC XY: 3791 AN XY: 725572

African (AFR) AF: 0.000868 AC: 29 AN: 33392

American (AMR) AF: 0.00366 AC: 163 AN: 44584

Ashkenazi Jewish (ASJ) AF: 0.00219 AC: 57 AN: 26082

East Asian (EAS) AF: 0.00 AC: 0 AN: 39640

South Asian (SAS) AF: 0.000604 AC: 52 AN: 86070

European-Finnish (FIN) AF: 0.00278 AC: 148 AN: 53308

Middle Eastern (MID) AF: 0.00225 AC: 13 AN: 5768

European-Non Finnish (NFE) AF: 0.00640 AC: 7102 AN: 1109298

Other (OTH) AF: 0.00435 AC: 262 AN: 60276

GnomAD4 genome AF: 0.00400 AC: 609 AN: 152348 Hom.: 1 Cov.: 32 AF XY: 0.00349 AC XY: 260 AN XY: 74498

African (AFR) AF: 0.00115 AC: 48 AN: 41580

American (AMR) AF: 0.00392 AC: 60 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.00346 AC: 12 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.000414 AC: 2 AN: 4826

European-Finnish (FIN) AF: 0.00311 AC: 33 AN: 10628

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00628 AC: 427 AN: 68034

Other (OTH) AF: 0.00237 AC: 5 AN: 2114

Alfa AF: 0.00191 Hom.: 0

Bravo AF: 0.00393

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.5
DANN	Benign	0.85
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs186635468; hg19: chr20-32376652;