rs13120250

Variant names:

• chr4-190005977-T-C
• rs13120250

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 0.383 in 151,936 control chromosomes in the GnomAD database, including 11,883 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 0.38 (11883 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.187
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 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: 0.383 AC: 58126 AN: 151818 Hom.: 11867 Cov.: 33

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.383 AC: 58182 AN: 151936 Hom.: 11883 Cov.: 33 AF XY: 0.381 AC XY: 28302 AN XY: 74230

African (AFR) AF: 0.523 AC: 21679 AN: 41416

American (AMR) AF: 0.302 AC: 4602 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1336 AN: 3466

East Asian (EAS) AF: 0.375 AC: 1934 AN: 5158

South Asian (SAS) AF: 0.341 AC: 1646 AN: 4824

European-Finnish (FIN) AF: 0.320 AC: 3377 AN: 10562

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22330 AN: 67932

Other (OTH) AF: 0.384 AC: 813 AN: 2116

Alfa AF: 0.347 Hom.: 1779

Bravo AF: 0.389

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.4
DANN	Benign	0.34
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs13120250; hg19: chr4-190927132;