4-115244948-C-T

Variant names:

• chr4-115244948-C-T
• rs1112531

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 0.598 in 151,258 control chromosomes in the GnomAD database, including 29,031 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 0.60 (29031 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.705 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: 0.598 AC: 90378 AN: 151146 Hom.: 29020 Cov.: 30

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.598 AC: 90418 AN: 151258 Hom.: 29031 Cov.: 30 AF XY: 0.599 AC XY: 44239 AN XY: 73876

African (AFR) AF: 0.351 AC: 14488 AN: 41288

American (AMR) AF: 0.668 AC: 10130 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1900 AN: 3458

East Asian (EAS) AF: 0.655 AC: 3352 AN: 5120

South Asian (SAS) AF: 0.562 AC: 2708 AN: 4818

European-Finnish (FIN) AF: 0.719 AC: 7563 AN: 10524

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48034 AN: 67582

Other (OTH) AF: 0.619 AC: 1300 AN: 2100

Alfa AF: 0.629 Hom.: 5113

Bravo AF: 0.590

Asia WGS AF: 0.586 AC: 2028 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.36
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1112531; hg19: chr4-116166104;