rs13141142

Variant names:

• chr4-156433098-T-C
• rs13141142

Your query was ambiguous. Multiple possible variants found:

• chr4-156433098-T-C
• chr4-156433098-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 0.06 in 152,232 control chromosomes in the GnomAD database, including 377 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 0.060 (377 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0833 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: 0.0601 AC: 9139 AN: 152112 Hom.: 374 Cov.: 32

Gnomad AFR AF: 0.0153

Gnomad AMI AF: 0.150

Gnomad AMR AF: 0.0611

Gnomad ASJ AF: 0.130

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.0893

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0851

Gnomad OTH AF: 0.0713

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

GnomAD4 genome AF: 0.0600 AC: 9140 AN: 152232 Hom.: 377 Cov.: 32 AF XY: 0.0585 AC XY: 4356 AN XY: 74434

Gnomad4 AFR AF: 0.0153

Gnomad4 AMR AF: 0.0615

Gnomad4 ASJ AF: 0.130

Gnomad4 EAS AF: 0.0184

Gnomad4 SAS AF: 0.0900

Gnomad4 FIN AF: 0.0452

Gnomad4 NFE AF: 0.0851

Gnomad4 OTH AF: 0.0701

Alfa AF: 0.0381 Hom.: 30

Bravo AF: 0.0597

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13141142; hg19: chr4-157354250;