rs17665418

Variant names:

• chr3-71800014-T-A
• rs17665418

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 0.0773 in 152,286 control chromosomes in the GnomAD database, including 517 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 0.077 (517 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 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: 0.0774 AC: 11784 AN: 152168 Hom.: 520 Cov.: 32

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.0658

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0817

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0780

Gnomad OTH AF: 0.0679

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

GnomAD4 genome AF: 0.0773 AC: 11777 AN: 152286 Hom.: 517 Cov.: 32 AF XY: 0.0785 AC XY: 5843 AN XY: 74464

African (AFR) AF: 0.0621 AC: 2582 AN: 41558

American (AMR) AF: 0.0658 AC: 1007 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 293 AN: 3470

East Asian (EAS) AF: 0.170 AC: 878 AN: 5178

South Asian (SAS) AF: 0.125 AC: 603 AN: 4824

European-Finnish (FIN) AF: 0.0817 AC: 866 AN: 10606

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0780 AC: 5307 AN: 68030

Other (OTH) AF: 0.0696 AC: 147 AN: 2112

Alfa AF: 0.0781 Hom.: 60

Bravo AF: 0.0770

Asia WGS AF: 0.154 AC: 534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.53
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs17665418; hg19: chr3-71849165;