rs2687481

chr7-126229068-G-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 0.257 in 152,020 control chromosomes in the GnomAD database, including 5,564 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 0.26 (5564 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 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: 0.257 AC: 39033 AN: 151902 Hom.: 5560 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.257 AC: 39064 AN: 152020 Hom.: 5564 Cov.: 33 AF XY: 0.260 AC XY: 19330 AN XY: 74288

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.235

Alfa AF: 0.200 Hom.: 2984

Bravo AF: 0.256

Asia WGS AF: 0.215 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.3
Dann	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2687481; hg19: chr7-125869122;