rs2621243

chr4-13009070-T-Cchr4-13009070-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 0.111 in 152,206 control chromosomes in the GnomAD database, including 1,498 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 0.11 (1498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16887 AN: 152088 Hom.: 1490 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.0645

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0228

Gnomad FIN AF: 0.0626

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0616

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.111 AC: 16945 AN: 152206 Hom.: 1498 Cov.: 32 AF XY: 0.109 AC XY: 8079 AN XY: 74426

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.0645

Gnomad4 ASJ AF: 0.0956

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0226

Gnomad4 FIN AF: 0.0626

Gnomad4 NFE AF: 0.0616

Gnomad4 OTH AF: 0.108

Alfa AF: 0.0665 Hom.: 467

Bravo AF: 0.120

Asia WGS AF: 0.0320 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.024
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2621243; hg19: chr4-13010694;