rs13120250

Positions:

• chr4-190005977-T-C

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 0.383 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.385

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.384

Alfa AF: 0.351 Hom.: 1312

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13120250; hg19: chr4-190927132;