4-170132368-G-A

Variant names:

• chr4-170132368-G-A
• rs11726248

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 0.0674 in 152,226 control chromosomes in the GnomAD database, including 494 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 0.067 (494 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.101 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: 0.0675 AC: 10261 AN: 152108 Hom.: 494 Cov.: 32

Gnomad AFR AF: 0.0183

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.0677

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0494

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.0793

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

GnomAD4 genome AF: 0.0674 AC: 10262 AN: 152226 Hom.: 494 Cov.: 32 AF XY: 0.0633 AC XY: 4713 AN XY: 74414

African (AFR) AF: 0.0182 AC: 757 AN: 41524

American (AMR) AF: 0.0675 AC: 1032 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3466

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5172

South Asian (SAS) AF: 0.0505 AC: 244 AN: 4830

European-Finnish (FIN) AF: 0.0470 AC: 498 AN: 10602

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7002 AN: 68020

Other (OTH) AF: 0.0794 AC: 168 AN: 2116

Alfa AF: 0.0633 Hom.: 172

Bravo AF: 0.0668

Asia WGS AF: 0.0330 AC: 116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.8
DANN	Benign	0.34
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs11726248; hg19: chr4-171053519;