11-123751378-T-C

Variant names:

• chr11-123751378-T-C
• rs11219274

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 0.543 in 152,012 control chromosomes in the GnomAD database, including 22,992 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 0.54 (22992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 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: 0.543 AC: 82461 AN: 151894 Hom.: 22989 Cov.: 32

Gnomad AFR AF: 0.586

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.543 AC: 82487 AN: 152012 Hom.: 22992 Cov.: 32 AF XY: 0.535 AC XY: 39716 AN XY: 74302

African (AFR) AF: 0.585 AC: 24261 AN: 41438

American (AMR) AF: 0.463 AC: 7065 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2056 AN: 3464

East Asian (EAS) AF: 0.203 AC: 1053 AN: 5182

South Asian (SAS) AF: 0.423 AC: 2032 AN: 4808

European-Finnish (FIN) AF: 0.531 AC: 5614 AN: 10568

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38604 AN: 67970

Other (OTH) AF: 0.559 AC: 1177 AN: 2104

Alfa AF: 0.558 Hom.: 5849

Bravo AF: 0.540

Asia WGS AF: 0.319 AC: 1110 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	4.8
DANN	Benign	0.82
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs11219274; hg19: chr11-123622086;