rs11982901

Variant names:

• chr7-128926700-C-T
• rs11982901

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 0.274 in 138,916 control chromosomes in the GnomAD database, including 5,727 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 0.27 (5727 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 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: 0.274 AC: 38008 AN: 138846 Hom.: 5726 Cov.: 23

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.274 AC: 38018 AN: 138916 Hom.: 5727 Cov.: 23 AF XY: 0.274 AC XY: 18270 AN XY: 66658

African (AFR) AF: 0.192 AC: 7055 AN: 36812

American (AMR) AF: 0.209 AC: 2818 AN: 13490

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 918 AN: 3360

East Asian (EAS) AF: 0.322 AC: 1470 AN: 4562

South Asian (SAS) AF: 0.299 AC: 1269 AN: 4246

European-Finnish (FIN) AF: 0.340 AC: 2692 AN: 7922

Middle Eastern (MID) AF: 0.277 AC: 71 AN: 256

European-Non Finnish (NFE) AF: 0.320 AC: 20916 AN: 65464

Other (OTH) AF: 0.246 AC: 478 AN: 1940

Alfa AF: 0.287 Hom.: 765

Bravo AF: 0.265

Asia WGS AF: 0.301 AC: 1041 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.48
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs11982901; hg19: chr7-128566754;