11-1145203-C-T

Variant names:

• chr11-1145203-C-T
• rs11245979

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 0.549 in 152,004 control chromosomes in the GnomAD database, including 25,746 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 0.55 (25746 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.946
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 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: 0.549 AC: 83399 AN: 151884 Hom.: 25759 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.701

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.617

Gnomad MID AF: 0.704

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.549 AC: 83385 AN: 152004 Hom.: 25746 Cov.: 32 AF XY: 0.543 AC XY: 40332 AN XY: 74264

African (AFR) AF: 0.250 AC: 10369 AN: 41462

American (AMR) AF: 0.516 AC: 7878 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2651 AN: 3468

East Asian (EAS) AF: 0.700 AC: 3617 AN: 5164

South Asian (SAS) AF: 0.548 AC: 2633 AN: 4808

European-Finnish (FIN) AF: 0.617 AC: 6512 AN: 10560

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47570 AN: 67976

Other (OTH) AF: 0.588 AC: 1236 AN: 2102

Alfa AF: 0.611 Hom.: 3689

Bravo AF: 0.532

Asia WGS AF: 0.530 AC: 1844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs11245979; hg19: chr11-1139111;