chr3-3638168-C-G

Variant names:

• chr3-3638168-C-G
• rs17034687

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 0.0793 in 152,222 control chromosomes in the GnomAD database, including 507 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 0.079 (507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0864 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: 0.0792 AC: 12052 AN: 152104 Hom.: 507 Cov.: 32

Gnomad AFR AF: 0.0885

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.0655

Gnomad ASJ AF: 0.0774

Gnomad EAS AF: 0.0106

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0828

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0850

Gnomad OTH AF: 0.0805

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

GnomAD4 genome AF: 0.0793 AC: 12068 AN: 152222 Hom.: 507 Cov.: 32 AF XY: 0.0771 AC XY: 5735 AN XY: 74432

African (AFR) AF: 0.0888 AC: 3686 AN: 41532

American (AMR) AF: 0.0654 AC: 1000 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0774 AC: 268 AN: 3464

East Asian (EAS) AF: 0.0106 AC: 55 AN: 5180

South Asian (SAS) AF: 0.0292 AC: 141 AN: 4824

European-Finnish (FIN) AF: 0.0828 AC: 878 AN: 10598

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0850 AC: 5782 AN: 68008

Other (OTH) AF: 0.0796 AC: 168 AN: 2110

Alfa AF: 0.0206 Hom.: 28

Bravo AF: 0.0794

Asia WGS AF: 0.0290 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.5
DANN	Benign	0.65
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs17034687; hg19: chr3-3679852;