rs208684

chr7-155814463-C-Achr7-155814463-C-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 0.747 in 151,970 control chromosomes in the GnomAD database, including 42,437 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 0.75 (42437 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.77 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: 0.746 AC: 113342 AN: 151852 Hom.: 42382 Cov.: 33

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.747 AC: 113456 AN: 151970 Hom.: 42437 Cov.: 33 AF XY: 0.745 AC XY: 55341 AN XY: 74246

Gnomad4 AFR AF: 0.716

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.759

Gnomad4 OTH AF: 0.719

Alfa AF: 0.755 Hom.: 10023

Bravo AF: 0.746

Asia WGS AF: 0.768 AC: 2672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.36
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs208684; hg19: chr7-155607157;