4-13009070-T-C

Variant names:

• chr4-13009070-T-C
• rs2621243

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 0.111 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
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.248 AC: 10294 AN: 41478

American (AMR) AF: 0.0645 AC: 987 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0956 AC: 332 AN: 3472

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5184

South Asian (SAS) AF: 0.0226 AC: 109 AN: 4828

European-Finnish (FIN) AF: 0.0626 AC: 664 AN: 10606

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0616 AC: 4192 AN: 68026

Other (OTH) AF: 0.108 AC: 228 AN: 2108

Alfa AF: 0.0874 Hom.: 1405

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2621243; hg19: chr4-13010694;