chr4-137416595-T-C

Variant names:

• chr4-137416595-T-C
• rs1320342

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 0.413 in 151,958 control chromosomes in the GnomAD database, including 13,043 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 0.41 (13043 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• 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 (EAS) allele frequency at 95% confidence interval = 0.505 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: 0.413 AC: 62681 AN: 151838 Hom.: 13045 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.587

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.383

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

GnomAD4 genome AF: 0.413 AC: 62690 AN: 151958 Hom.: 13043 Cov.: 31 AF XY: 0.414 AC XY: 30733 AN XY: 74268

African (AFR) AF: 0.377 AC: 15608 AN: 41446

American (AMR) AF: 0.437 AC: 6666 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1137 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2679 AN: 5140

South Asian (SAS) AF: 0.274 AC: 1318 AN: 4814

European-Finnish (FIN) AF: 0.512 AC: 5409 AN: 10562

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28411 AN: 67952

Other (OTH) AF: 0.380 AC: 802 AN: 2110

Alfa AF: 0.403 Hom.: 6613

Bravo AF: 0.410

Asia WGS AF: 0.387 AC: 1347 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.64
DANN	Benign	0.71
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs1320342; hg19: chr4-138337749;