rs1506981

Variant names:

• chr11-6757840-A-G
• rs1506981

Your query was ambiguous. Multiple possible variants found:

• chr11-6757840-A-G
• chr11-6757840-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.345 AC: 14315 AN: 41474

American (AMR) AF: 0.358 AC: 5469 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.502 AC: 1740 AN: 3468

East Asian (EAS) AF: 0.480 AC: 2481 AN: 5166

South Asian (SAS) AF: 0.363 AC: 1751 AN: 4822

European-Finnish (FIN) AF: 0.393 AC: 4151 AN: 10554

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26030 AN: 67956

Other (OTH) AF: 0.396 AC: 837 AN: 2114

Alfa AF: 0.381 Hom.: 22864

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
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs1506981; hg19: chr11-6779071;