rs893108

Variant names:

• chr7-155141738-G-A
• rs893108

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 0.158 in 152,120 control chromosomes in the GnomAD database, including 2,328 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 0.16 (2328 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24035 AN: 152000 Hom.: 2322 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.158 AC: 24051 AN: 152120 Hom.: 2328 Cov.: 32 AF XY: 0.160 AC XY: 11909 AN XY: 74376

African (AFR) AF: 0.0478 AC: 1984 AN: 41532

American (AMR) AF: 0.209 AC: 3199 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 746 AN: 3466

East Asian (EAS) AF: 0.109 AC: 564 AN: 5174

South Asian (SAS) AF: 0.210 AC: 1009 AN: 4804

European-Finnish (FIN) AF: 0.167 AC: 1772 AN: 10592

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.210 AC: 14268 AN: 67958

Other (OTH) AF: 0.175 AC: 370 AN: 2110

Alfa AF: 0.175 Hom.: 315

Bravo AF: 0.155

Asia WGS AF: 0.155 AC: 538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.9
DANN	Benign	0.80
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs893108; hg19: chr7-154933448;