11-120994213-T-C

Variant names:

• chr11-120994213-T-C
• rs1944522

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 0.471 in 152,034 control chromosomes in the GnomAD database, including 17,278 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 0.47 (17278 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.533 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: 0.471 AC: 71539 AN: 151916 Hom.: 17267 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.543

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.471 AC: 71597 AN: 152034 Hom.: 17278 Cov.: 31 AF XY: 0.473 AC XY: 35144 AN XY: 74322

African (AFR) AF: 0.383 AC: 15881 AN: 41450

American (AMR) AF: 0.543 AC: 8295 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1840 AN: 3466

East Asian (EAS) AF: 0.351 AC: 1814 AN: 5172

South Asian (SAS) AF: 0.420 AC: 2026 AN: 4826

European-Finnish (FIN) AF: 0.541 AC: 5721 AN: 10574

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.505 AC: 34306 AN: 67948

Other (OTH) AF: 0.505 AC: 1069 AN: 2116

Alfa AF: 0.491 Hom.: 76517

Bravo AF: 0.468

Asia WGS AF: 0.363 AC: 1265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.31
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1944522; hg19: chr11-120864922;