chr4-171230409-G-A

Variant names:

• chr4-171230409-G-A
• rs958357

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 0.888 in 152,236 control chromosomes in the GnomAD database, including 60,125 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 0.89 (60125 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 0 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 = 0.911 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: 0.888 AC: 135097 AN: 152118 Hom.: 60077 Cov.: 32

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.892

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

GnomAD4 genome AF: 0.888 AC: 135201 AN: 152236 Hom.: 60125 Cov.: 32 AF XY: 0.892 AC XY: 66393 AN XY: 74420

African (AFR) AF: 0.862 AC: 35793 AN: 41522

American (AMR) AF: 0.924 AC: 14132 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3072 AN: 3472

East Asian (EAS) AF: 0.932 AC: 4825 AN: 5176

South Asian (SAS) AF: 0.924 AC: 4458 AN: 4824

European-Finnish (FIN) AF: 0.926 AC: 9828 AN: 10612

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.884 AC: 60150 AN: 68018

Other (OTH) AF: 0.892 AC: 1888 AN: 2116

Alfa AF: 0.878 Hom.: 3594

Bravo AF: 0.887

Asia WGS AF: 0.910 AC: 3160 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.69
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs958357; hg19: chr4-172151560;