chr4-38334202-C-T

Variant names:

• chr4-38334202-C-T
• rs1487630

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 0.141 in 152,086 control chromosomes in the GnomAD database, including 1,992 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 0.14 (1992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 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: 0.142 AC: 21514 AN: 151966 Hom.: 1993 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.0908

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.0344

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.141 AC: 21518 AN: 152086 Hom.: 1992 Cov.: 32 AF XY: 0.141 AC XY: 10470 AN XY: 74340

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.0905

Gnomad4 ASJ AF: 0.102

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.0344

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.143

Alfa AF: 0.114 Hom.: 671

Bravo AF: 0.146

Asia WGS AF: 0.203 AC: 707 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.097
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1487630; hg19: chr4-38335823;