chr7-155101164-G-A

Variant names:

• chr7-155101164-G-A
• rs893109

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 0.283 in 152,124 control chromosomes in the GnomAD database, including 6,480 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 0.28 (6480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.991
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 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: 0.284 AC: 43109 AN: 152006 Hom.: 6476 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.415

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.283 AC: 43121 AN: 152124 Hom.: 6480 Cov.: 33 AF XY: 0.286 AC XY: 21284 AN XY: 74398

African (AFR) AF: 0.210 AC: 8701 AN: 41508

American (AMR) AF: 0.292 AC: 4458 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 896 AN: 3470

East Asian (EAS) AF: 0.535 AC: 2756 AN: 5156

South Asian (SAS) AF: 0.353 AC: 1703 AN: 4820

European-Finnish (FIN) AF: 0.309 AC: 3279 AN: 10596

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20301 AN: 67986

Other (OTH) AF: 0.281 AC: 591 AN: 2104

Alfa AF: 0.291 Hom.: 3667

Bravo AF: 0.284

Asia WGS AF: 0.389 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.66
DANN	Benign	0.81
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs893109; hg19: chr7-154892874;