11-80008630-T-C

Variant names:

• chr11-80008630-T-C
• rs7950475

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 0.0688 in 152,206 control chromosomes in the GnomAD database, including 1,085 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 0.069 (1085 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 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: 0.0687 AC: 10454 AN: 152088 Hom.: 1084 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0302

Gnomad ASJ AF: 0.0288

Gnomad EAS AF: 0.0112

Gnomad SAS AF: 0.0220

Gnomad FIN AF: 0.0000942

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.00207

Gnomad OTH AF: 0.0568

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

GnomAD4 genome AF: 0.0688 AC: 10476 AN: 152206 Hom.: 1085 Cov.: 33 AF XY: 0.0673 AC XY: 5010 AN XY: 74432

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.0302

Gnomad4 ASJ AF: 0.0288

Gnomad4 EAS AF: 0.0110

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.0000942

Gnomad4 NFE AF: 0.00207

Gnomad4 OTH AF: 0.0562

Alfa AF: 0.0145 Hom.: 25

Bravo AF: 0.0787

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	7.6
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7950475; hg19: chr11-79719673;