rs141371905

Variant names:

• chr15-42435462-C-G
• rs141371905
• NM_001366845.3:c.4803G>C

Your query was ambiguous. Multiple possible variants found:

• chr15-42435462-C-G
• chr15-42435462-C-T

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_001366845.3(ZNF106):​c.4803G>C​(p.Leu1601Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00392 in 1,614,142 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0027 (2 hom., cov: 32)
  • Exomes 𝑓: 0.0040 (14 hom.)
• Consequence: ZNF106 NM_001366845.3 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.76
• Publications: 2 publications found

Genes affected

ZNF106 (HGNC:12886): (zinc finger protein 106) Enables RNA binding activity. Predicted to be involved in insulin receptor signaling pathway. Predicted to be located in nuclear speck and nucleolus. Predicted to be active in cytosol and membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP6: Variant 15-42435462-C-G is Benign according to our data. Variant chr15-42435462-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 2645238.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001366845.3. 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
	ZNF106	NM_001366845.3	MANE Select	c.4803G>C	p.Leu1601Leu	synonymous	Exon 14 of 22	NP_001353774.1	H3BSS6
	ZNF106	NM_022473.3		c.4734G>C	p.Leu1578Leu	synonymous	Exon 11 of 19	NP_071918.1	Q9H2Y7-1
	ZNF106	NM_001381993.1		c.4602G>C	p.Leu1534Leu	synonymous	Exon 13 of 21	NP_001368922.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF106	ENST00000564754.7	TSL:1 MANE Select	c.4803G>C	p.Leu1601Leu	synonymous	Exon 14 of 22	ENSP00000456845.2	H3BSS6
	ZNF106	ENST00000263805.8	TSL:1	c.4734G>C	p.Leu1578Leu	synonymous	Exon 11 of 19	ENSP00000263805.4	Q9H2Y7-1
	ZNF106	ENST00000565380.5	TSL:1	c.2418G>C	p.Leu806Leu	synonymous	Exon 12 of 20	ENSP00000455674.1	Q9H2Y7-2

Frequencies

GnomAD3 genomes AF: 0.00271 AC: 412 AN: 152136 Hom.: 2 Cov.: 32

Gnomad AFR AF: 0.000893

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.00183

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.00349

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00431

Gnomad OTH AF: 0.00192

GnomAD2 exomes AF: 0.00321 AC: 806 AN: 251476 AF XY: 0.00324

Gnomad AFR exome AF: 0.000923

Gnomad AMR exome AF: 0.00332

Gnomad ASJ exome AF: 0.00238

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00342

Gnomad NFE exome AF: 0.00457

Gnomad OTH exome AF: 0.00440

GnomAD4 exome AF: 0.00405 AC: 5916 AN: 1461888 Hom.: 14 Cov.: 31 AF XY: 0.00394 AC XY: 2864 AN XY: 727244

African (AFR) AF: 0.000806 AC: 27 AN: 33480

American (AMR) AF: 0.00306 AC: 137 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.00187 AC: 49 AN: 26136

East Asian (EAS) AF: 0.00 AC: 0 AN: 39700

South Asian (SAS) AF: 0.00108 AC: 93 AN: 86258

European-Finnish (FIN) AF: 0.00335 AC: 179 AN: 53420

Middle Eastern (MID) AF: 0.00104 AC: 6 AN: 5768

European-Non Finnish (NFE) AF: 0.00471 AC: 5239 AN: 1112006

Other (OTH) AF: 0.00308 AC: 186 AN: 60396

GnomAD4 genome AF: 0.00271 AC: 412 AN: 152254 Hom.: 2 Cov.: 32 AF XY: 0.00286 AC XY: 213 AN XY: 74450

African (AFR) AF: 0.000891 AC: 37 AN: 41546

American (AMR) AF: 0.00183 AC: 28 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5190

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4822

European-Finnish (FIN) AF: 0.00349 AC: 37 AN: 10606

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00431 AC: 293 AN: 68012

Other (OTH) AF: 0.00190 AC: 4 AN: 2106

Alfa AF: 0.00361 Hom.: 1

Bravo AF: 0.00264

Asia WGS AF: 0.000577 AC: 3 AN: 3478

EpiCase AF: 0.00344

EpiControl AF: 0.00409

ClinVar

ClinVar submissions as Germline

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	15
DANN	Benign	0.40
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.31		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.31		Position offset: -10

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

Other links and lift over

dbSNP: rs141371905; hg19: chr15-42727660;