4-130140798-T-C

Variant names:

• chr4-130140798-T-C
• rs2172478

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 0.706 in 151,216 control chromosomes in the GnomAD database, including 38,020 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 0.71 (38020 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.706 AC: 106667 AN: 151098 Hom.: 37984 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.706 AC: 106753 AN: 151216 Hom.: 38020 Cov.: 32 AF XY: 0.699 AC XY: 51619 AN XY: 73878

African (AFR) AF: 0.693 AC: 28672 AN: 41362

American (AMR) AF: 0.682 AC: 10292 AN: 15096

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2406 AN: 3450

East Asian (EAS) AF: 0.469 AC: 2416 AN: 5150

South Asian (SAS) AF: 0.558 AC: 2689 AN: 4816

European-Finnish (FIN) AF: 0.683 AC: 7205 AN: 10548

Middle Eastern (MID) AF: 0.734 AC: 213 AN: 290

European-Non Finnish (NFE) AF: 0.752 AC: 50781 AN: 67496

Other (OTH) AF: 0.709 AC: 1487 AN: 2098

Alfa AF: 0.688 Hom.: 3857

Bravo AF: 0.707

Asia WGS AF: 0.519 AC: 1804 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.42
PhyloP100		-0.044

Splicing

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

Other links and lift over

dbSNP: rs2172478; hg19: chr4-131061953;