rs191392302

Variant names:

• chr17-41797709-T-G
• rs191392302

Variant summary

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

The variant allele was found at a frequency of 0.0341 in 150,170 control chromosomes in the GnomAD database, including 155 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 (155 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.868
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0826 is higher than 0.05.

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: 0.0339 AC: 5091 AN: 150058 Hom.: 147 Cov.: 31

Gnomad AFR AF: 0.0844

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0128

Gnomad ASJ AF: 0.00606

Gnomad EAS AF: 0.0391

Gnomad SAS AF: 0.0267

Gnomad FIN AF: 0.0404

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00951

Gnomad OTH AF: 0.0227

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

GnomAD4 genome AF: 0.0341 AC: 5118 AN: 150170 Hom.: 155 Cov.: 31 AF XY: 0.0354 AC XY: 2595 AN XY: 73388

African (AFR) AF: 0.0849 AC: 3398 AN: 40002

American (AMR) AF: 0.0128 AC: 194 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.00606 AC: 21 AN: 3468

East Asian (EAS) AF: 0.0388 AC: 199 AN: 5130

South Asian (SAS) AF: 0.0267 AC: 128 AN: 4794

European-Finnish (FIN) AF: 0.0404 AC: 424 AN: 10494

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 288

European-Non Finnish (NFE) AF: 0.00950 AC: 644 AN: 67790

Other (OTH) AF: 0.0225 AC: 47 AN: 2092

Alfa AF: 0.0222 Hom.: 111

Bravo AF: 0.0349

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.23
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs191392302; hg19: chr17-39953961; COSMIC: COSV62680376;