4-171462288-C-T

Variant names:

• chr4-171462288-C-T
• rs2178299

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 0.657 in 151,970 control chromosomes in the GnomAD database, including 34,975 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 0.66 (34975 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.811
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 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: 0.657 AC: 99835 AN: 151852 Hom.: 34969 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.694

Gnomad FIN AF: 0.819

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.749

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.657 AC: 99873 AN: 151970 Hom.: 34975 Cov.: 32 AF XY: 0.666 AC XY: 49479 AN XY: 74270

African (AFR) AF: 0.391 AC: 16194 AN: 41400

American (AMR) AF: 0.765 AC: 11687 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2547 AN: 3468

East Asian (EAS) AF: 0.857 AC: 4439 AN: 5180

South Asian (SAS) AF: 0.694 AC: 3342 AN: 4814

European-Finnish (FIN) AF: 0.819 AC: 8653 AN: 10568

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.749 AC: 50871 AN: 67944

Other (OTH) AF: 0.663 AC: 1401 AN: 2112

Alfa AF: 0.721 Hom.: 17453

Bravo AF: 0.641

Asia WGS AF: 0.784 AC: 2698 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.51
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2178299; hg19: chr4-172383439;