4-137919841-T-C

Variant names:

• chr4-137919841-T-C
• rs13128867

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 0.206 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0924 AC: 3839 AN: 41554

American (AMR) AF: 0.274 AC: 4176 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 462 AN: 3470

East Asian (EAS) AF: 0.722 AC: 3725 AN: 5158

South Asian (SAS) AF: 0.344 AC: 1661 AN: 4824

European-Finnish (FIN) AF: 0.242 AC: 2564 AN: 10576

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14272 AN: 67966

Other (OTH) AF: 0.202 AC: 427 AN: 2110

Alfa AF: 0.209 Hom.: 10148

Bravo AF: 0.204

Asia WGS AF: 0.464 AC: 1613 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.76
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs13128867; hg19: chr4-138840995;