11-2173580-T-C

Variant names:

• chr11-2173580-T-C
• rs7119275

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 0.691 in 152,008 control chromosomes in the GnomAD database, including 36,672 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 0.69 (36672 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 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: 0.691 AC: 104912 AN: 151890 Hom.: 36650 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.691 AC: 104984 AN: 152008 Hom.: 36672 Cov.: 32 AF XY: 0.696 AC XY: 51691 AN XY: 74302

Gnomad4 AFR AF: 0.765

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.718

Alfa AF: 0.659 Hom.: 4281

Bravo AF: 0.696

Asia WGS AF: 0.858 AC: 2986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7119275; hg19: chr11-2194810;