4-13100727-G-T

Variant names:

• chr4-13100727-G-T
• rs13122273

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 0.167 in 152,158 control chromosomes in the GnomAD database, including 2,720 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 0.17 (2720 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 4 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 (SAS) allele frequency at 95% confidence interval = 0.35 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: 0.167 AC: 25381 AN: 152038 Hom.: 2722 Cov.: 32

Gnomad AFR AF: 0.0430

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.167 AC: 25371 AN: 152158 Hom.: 2720 Cov.: 32 AF XY: 0.168 AC XY: 12494 AN XY: 74396

African (AFR) AF: 0.0428 AC: 1779 AN: 41562

American (AMR) AF: 0.147 AC: 2241 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3464

East Asian (EAS) AF: 0.262 AC: 1347 AN: 5138

South Asian (SAS) AF: 0.364 AC: 1750 AN: 4810

European-Finnish (FIN) AF: 0.189 AC: 1999 AN: 10588

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.221 AC: 15058 AN: 67986

Other (OTH) AF: 0.154 AC: 325 AN: 2112

Alfa AF: 0.190 Hom.: 7783

Bravo AF: 0.157

Asia WGS AF: 0.292 AC: 1017 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	0.29
DANN	Benign	0.58
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs13122273; hg19: chr4-13102351;