rs1506981

chr11-6757840-A-Gchr11-6757840-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 0.377 in 152,038 control chromosomes in the GnomAD database, including 10,920 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 0.38 (10920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

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 (EAS) allele frequency at 95% confidence interval = 0.465 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: 0.377 AC: 57294 AN: 151920 Hom.: 10911 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.502

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.377 AC: 57337 AN: 152038 Hom.: 10920 Cov.: 32 AF XY: 0.378 AC XY: 28060 AN XY: 74298

Gnomad4 AFR AF: 0.345

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.502

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.393

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.396

Alfa AF: 0.385 Hom.: 15560

Bravo AF: 0.375

Asia WGS AF: 0.401 AC: 1395 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.8
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1506981; hg19: chr11-6779071;