rs3760396

Variant names:

• chr17-34254422-G-C
• rs3760396

Your query was ambiguous. Multiple possible variants found:

• chr17-34254422-G-C
• chr17-34254422-G-T

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 0.151 in 152,180 control chromosomes in the GnomAD database, including 2,164 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 0.15 (2164 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.662
• Publications: 41 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 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: 0.151 AC: 22995 AN: 152062 Hom.: 2163 Cov.: 32

Gnomad AFR AF: 0.0551

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0841

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.151 AC: 22997 AN: 152180 Hom.: 2164 Cov.: 32 AF XY: 0.148 AC XY: 11033 AN XY: 74390

African (AFR) AF: 0.0550 AC: 2285 AN: 41536

American (AMR) AF: 0.112 AC: 1713 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3472

East Asian (EAS) AF: 0.0839 AC: 434 AN: 5170

South Asian (SAS) AF: 0.0941 AC: 454 AN: 4824

European-Finnish (FIN) AF: 0.207 AC: 2188 AN: 10594

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14777 AN: 67988

Other (OTH) AF: 0.133 AC: 281 AN: 2110

Alfa AF: 0.131 Hom.: 277

Bravo AF: 0.140

Asia WGS AF: 0.0820 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.0
DANN	Benign	0.61
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs3760396; hg19: chr17-32581441;