rs17611827

Variant names:

• chr16-3317061-G-A
• rs17611827
• NM_001302109.2:c.934+39G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-3317061-G-A
• chr16-3317061-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001302109.2(ZNF75A):​c.934+39G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 1,575,034 control chromosomes in the GnomAD database, including 39,200 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.21 (3724 hom., cov: 32)
  • Exomes 𝑓: 0.22 (35476 hom.)
• Consequence: ZNF75A NM_001302109.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 20 publications found

Genes affected

ZNF75A (HGNC:13146): (zinc finger protein 75A) Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001302109.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF75A	NM_001302109.2	MANE Select	c.934+39G>A		intron	N/A	NP_001289038.1
	ZNF75A	NM_001324041.1		c.934+39G>A		intron	N/A	NP_001310970.1
	ZNF75A	NM_153028.4		c.211+39G>A		intron	N/A	NP_694573.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ZNF75A	ENST00000669516.2	MANE Select	c.934+39G>A		intron	N/A	ENSP00000499415.1
	ZNF75A	ENST00000617839.1	TSL:1	c.211+39G>A		intron	N/A	ENSP00000482769.1
	ZNF75A	ENST00000574298.6	TSL:2	c.211+39G>A		intron	N/A	ENSP00000459566.1

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32563 AN: 151930 Hom.: 3723 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.0977

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.202

GnomAD2 exomes AF: 0.221 AC: 51624 AN: 233216 AF XY: 0.213

Gnomad AFR exome AF: 0.183

Gnomad AMR exome AF: 0.346

Gnomad ASJ exome AF: 0.208

Gnomad EAS exome AF: 0.0426

Gnomad FIN exome AF: 0.289

Gnomad NFE exome AF: 0.236

Gnomad OTH exome AF: 0.224

GnomAD4 exome AF: 0.217 AC: 308729 AN: 1422986 Hom.: 35476 Cov.: 25 AF XY: 0.213 AC XY: 150887 AN XY: 708650

African (AFR) AF: 0.179 AC: 5748 AN: 32180

American (AMR) AF: 0.328 AC: 13222 AN: 40360

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 4992 AN: 25238

East Asian (EAS) AF: 0.0380 AC: 1502 AN: 39522

South Asian (SAS) AF: 0.106 AC: 8710 AN: 82184

European-Finnish (FIN) AF: 0.281 AC: 14948 AN: 53214

Middle Eastern (MID) AF: 0.112 AC: 630 AN: 5646

European-Non Finnish (NFE) AF: 0.228 AC: 247294 AN: 1085666

Other (OTH) AF: 0.198 AC: 11683 AN: 58976

GnomAD4 genome AF: 0.214 AC: 32578 AN: 152048 Hom.: 3724 Cov.: 32 AF XY: 0.215 AC XY: 16015 AN XY: 74330

African (AFR) AF: 0.188 AC: 7792 AN: 41500

American (AMR) AF: 0.277 AC: 4234 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 665 AN: 3470

East Asian (EAS) AF: 0.0373 AC: 193 AN: 5180

South Asian (SAS) AF: 0.0976 AC: 470 AN: 4816

European-Finnish (FIN) AF: 0.282 AC: 2973 AN: 10540

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15607 AN: 67962

Other (OTH) AF: 0.199 AC: 420 AN: 2110

Alfa AF: 0.219 Hom.: 1638

Bravo AF: 0.216

Asia WGS AF: 0.0810 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.60
PhyloP100		-0.35
Mutation Taster		=100/0	polymorphism (auto)

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: rs17611827; hg19: chr16-3367061; COSMIC: COSV73039566; COSMIC: COSV73039566;