rs11982901

chr7-128926700-C-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 0.274 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;