rs855648

Variant names:

• chr7-149751163-A-T
• rs855648

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;