11-131354693-G-A

Variant names:

• chr11-131354693-G-A
• rs4128594

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 0.323 in 152,078 control chromosomes in the GnomAD database, including 8,471 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 0.32 (8471 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 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: 0.324 AC: 49173 AN: 151960 Hom.: 8473 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.298

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.323 AC: 49182 AN: 152078 Hom.: 8471 Cov.: 32 AF XY: 0.325 AC XY: 24135 AN XY: 74358

African (AFR) AF: 0.204 AC: 8482 AN: 41494

American (AMR) AF: 0.360 AC: 5501 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1562 AN: 3472

East Asian (EAS) AF: 0.431 AC: 2226 AN: 5164

South Asian (SAS) AF: 0.428 AC: 2061 AN: 4812

European-Finnish (FIN) AF: 0.311 AC: 3287 AN: 10582

Middle Eastern (MID) AF: 0.520 AC: 153 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24853 AN: 67968

Other (OTH) AF: 0.373 AC: 786 AN: 2108

Alfa AF: 0.355 Hom.: 15207

Bravo AF: 0.323

Asia WGS AF: 0.361 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.61
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs4128594; hg19: chr11-131224588; COSMIC: COSV74104572;