chr7-155088528-C-T

Variant names:

• chr7-155088528-C-T
• rs893112

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 0.777 in 152,022 control chromosomes in the GnomAD database, including 46,878 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 0.78 (46878 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118048 AN: 151902 Hom.: 46823 Cov.: 31

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.777 AC: 118154 AN: 152022 Hom.: 46878 Cov.: 31 AF XY: 0.774 AC XY: 57488 AN XY: 74304

African (AFR) AF: 0.946 AC: 39249 AN: 41492

American (AMR) AF: 0.780 AC: 11919 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2579 AN: 3464

East Asian (EAS) AF: 0.780 AC: 4021 AN: 5152

South Asian (SAS) AF: 0.701 AC: 3359 AN: 4794

European-Finnish (FIN) AF: 0.630 AC: 6656 AN: 10568

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47980 AN: 67952

Other (OTH) AF: 0.753 AC: 1588 AN: 2110

Alfa AF: 0.736 Hom.: 5253

Bravo AF: 0.797

Asia WGS AF: 0.699 AC: 2433 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.4
DANN	Benign	0.48
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs893112; hg19: chr7-154880238;