rs855648

Variant names:

• chr7-149751163-A-T
• rs855648

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 0.688 in 152,058 control chromosomes in the GnomAD database, including 36,426 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 0.69 (36426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.688 AC: 104560 AN: 151940 Hom.: 36389 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.592

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.839

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.688 AC: 104649 AN: 152058 Hom.: 36426 Cov.: 32 AF XY: 0.691 AC XY: 51315 AN XY: 74280

African (AFR) AF: 0.742 AC: 30783 AN: 41478

American (AMR) AF: 0.765 AC: 11702 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2133 AN: 3472

East Asian (EAS) AF: 0.839 AC: 4325 AN: 5152

South Asian (SAS) AF: 0.737 AC: 3545 AN: 4810

European-Finnish (FIN) AF: 0.598 AC: 6318 AN: 10562

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43663 AN: 67982

Other (OTH) AF: 0.687 AC: 1450 AN: 2110

Alfa AF: 0.679 Hom.: 4391

Bravo AF: 0.703

Asia WGS AF: 0.771 AC: 2683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.063
DANN	Benign	0.77
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs855648; hg19: chr7-149448252;