chr4-137306455-C-T

Variant names:

• chr4-137306455-C-T
• rs987360

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 0.498 in 151,588 control chromosomes in the GnomAD database, including 19,917 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 0.50 (19917 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.667 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: 0.498 AC: 75424 AN: 151470 Hom.: 19877 Cov.: 32

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.443

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.434

Gnomad FIN AF: 0.405

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.498 AC: 75521 AN: 151588 Hom.: 19917 Cov.: 32 AF XY: 0.499 AC XY: 36934 AN XY: 74062

African (AFR) AF: 0.674 AC: 27882 AN: 41398

American (AMR) AF: 0.443 AC: 6717 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1615 AN: 3458

East Asian (EAS) AF: 0.632 AC: 3232 AN: 5110

South Asian (SAS) AF: 0.435 AC: 2097 AN: 4818

European-Finnish (FIN) AF: 0.405 AC: 4266 AN: 10538

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28037 AN: 67780

Other (OTH) AF: 0.514 AC: 1083 AN: 2106

Alfa AF: 0.450 Hom.: 45181

Bravo AF: 0.512

Asia WGS AF: 0.534 AC: 1858 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	0.19
DANN	Benign	0.65
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs987360; hg19: chr4-138227609;