rs855648

chr7-149751163-A-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.839

Gnomad4 SAS AF: 0.737

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.642

Gnomad4 OTH AF: 0.687

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.063
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs855648; hg19: chr7-149448252;