rs17622673

Variant names:

• chr6-103087861-T-C
• rs17622673

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 0.0832 in 152,128 control chromosomes in the GnomAD database, including 552 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 0.083 (552 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.0942 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: 0.0831 AC: 12637 AN: 152010 Hom.: 551 Cov.: 31

Gnomad AFR AF: 0.0967

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.0913

Gnomad ASJ AF: 0.0567

Gnomad EAS AF: 0.000388

Gnomad SAS AF: 0.0431

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0897

Gnomad OTH AF: 0.0769

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

GnomAD4 genome AF: 0.0832 AC: 12650 AN: 152128 Hom.: 552 Cov.: 31 AF XY: 0.0793 AC XY: 5894 AN XY: 74362

African (AFR) AF: 0.0967 AC: 4015 AN: 41510

American (AMR) AF: 0.0914 AC: 1395 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0567 AC: 197 AN: 3472

East Asian (EAS) AF: 0.000389 AC: 2 AN: 5148

South Asian (SAS) AF: 0.0433 AC: 209 AN: 4822

European-Finnish (FIN) AF: 0.0448 AC: 475 AN: 10608

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0896 AC: 6095 AN: 67990

Other (OTH) AF: 0.0766 AC: 161 AN: 2102

Alfa AF: 0.0829 Hom.: 68

Bravo AF: 0.0882

Asia WGS AF: 0.0230 AC: 80 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9
DANN	Benign	0.85
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs17622673; hg19: chr6-103535736;