rs11982901

Variant names:

• chr7-128926700-C-T
• rs11982901

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 0.274 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.273

Gnomad4 EAS AF: 0.322

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.246

Alfa AF: 0.291 Hom.: 746

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11982901; hg19: chr7-128566754;