chr4-13097258-C-T

Variant names:

• chr4-13097258-C-T
• rs512244

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.879 in 152,220 control chromosomes in the GnomAD database, including 58,903 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 0.88 (58903 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.879 AC: 133736 AN: 152102 Hom.: 58859 Cov.: 33

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.907

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.879 AC: 133838 AN: 152220 Hom.: 58903 Cov.: 33 AF XY: 0.879 AC XY: 65415 AN XY: 74424

Gnomad4 AFR AF: 0.894

Gnomad4 AMR AF: 0.908

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.928

Gnomad4 FIN AF: 0.816

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.884

Alfa AF: 0.872 Hom.: 68429

Bravo AF: 0.887

Asia WGS AF: 0.968 AC: 3364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.14
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs512244; hg19: chr4-13098882;