4-188064339-T-C

Variant names:

• chr4-188064339-T-C
• rs11132507

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 0.65 in 151,434 control chromosomes in the GnomAD database, including 32,424 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 0.65 (32424 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.873 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: 0.650 AC: 98419 AN: 151316 Hom.: 32395 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.650 AC: 98500 AN: 151434 Hom.: 32424 Cov.: 32 AF XY: 0.648 AC XY: 47925 AN XY: 73956

African (AFR) AF: 0.569 AC: 23481 AN: 41276

American (AMR) AF: 0.667 AC: 10145 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2689 AN: 3456

East Asian (EAS) AF: 0.894 AC: 4609 AN: 5154

South Asian (SAS) AF: 0.535 AC: 2576 AN: 4812

European-Finnish (FIN) AF: 0.621 AC: 6491 AN: 10452

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46269 AN: 67764

Other (OTH) AF: 0.683 AC: 1438 AN: 2106

Alfa AF: 0.674 Hom.: 123014

Bravo AF: 0.654

Asia WGS AF: 0.717 AC: 2489 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	2.8
DANN	Benign	0.47
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs11132507; hg19: chr4-188985493;