chr17-3996349-G-A

Variant names:

• chr17-3996349-G-A
• rs9914203

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0343 in 151,918 control chromosomes in the GnomAD database, including 116 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 0.034 (116 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0343 (5208/151918) while in subpopulation NFE AF = 0.0503 (3420/67944). AF 95% confidence interval is 0.0489. There are 116 homozygotes in GnomAd4. There are 2460 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 116 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0343 AC: 5207 AN: 151800 Hom.: 116 Cov.: 32

Gnomad AFR AF: 0.00905

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0450

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0373

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0503

Gnomad OTH AF: 0.0455

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0343 AC: 5208 AN: 151918 Hom.: 116 Cov.: 32 AF XY: 0.0331 AC XY: 2460 AN XY: 74220

African (AFR) AF: 0.00902 AC: 374 AN: 41462

American (AMR) AF: 0.0371 AC: 566 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.0450 AC: 156 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0141 AC: 68 AN: 4820

European-Finnish (FIN) AF: 0.0373 AC: 390 AN: 10468

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0503 AC: 3420 AN: 67944

Other (OTH) AF: 0.0450 AC: 95 AN: 2112

Alfa AF: 0.0409 Hom.: 21

Bravo AF: 0.0325

Asia WGS AF: 0.00924 AC: 33 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.26
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs9914203; hg19: chr17-3899643; COSMIC: COSV60070699;