4-137919841-T-C

Variant names:

• chr4-137919841-T-C
• rs13128867

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 0.206 in 152,128 control chromosomes in the GnomAD database, including 4,349 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 0.21 (4349 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 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: 0.206 AC: 31361 AN: 152010 Hom.: 4351 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.206 AC: 31364 AN: 152128 Hom.: 4349 Cov.: 32 AF XY: 0.212 AC XY: 15782 AN XY: 74368

Gnomad4 AFR AF: 0.0924

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.344

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.210

Gnomad4 OTH AF: 0.202

Alfa AF: 0.213 Hom.: 5777

Bravo AF: 0.204

Asia WGS AF: 0.464 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13128867; hg19: chr4-138840995;