rs13150247

Variant names:

• chr4-99720811-T-C
• rs13150247

Your query was ambiguous. Multiple possible variants found:

• chr4-99720811-T-C
• chr4-99720811-T-G

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 0.103 in 152,138 control chromosomes in the GnomAD database, including 1,275 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 0.10 (1275 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 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: 0.103 AC: 15645 AN: 152020 Hom.: 1262 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.0747

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.0274

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.0450

Gnomad FIN AF: 0.0223

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0485

Gnomad OTH AF: 0.0883

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

GnomAD4 genome AF: 0.103 AC: 15693 AN: 152138 Hom.: 1275 Cov.: 32 AF XY: 0.102 AC XY: 7588 AN XY: 74394

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.0274

Gnomad4 EAS AF: 0.192

Gnomad4 SAS AF: 0.0448

Gnomad4 FIN AF: 0.0223

Gnomad4 NFE AF: 0.0485

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0594 Hom.: 226

Bravo AF: 0.116

Asia WGS AF: 0.113 AC: 390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13150247; hg19: chr4-100641968;