rs4387258

Variant names:

• chr10-29198436-G-A
• rs4387258

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 0.145 in 151,514 control chromosomes in the GnomAD database, including 1,936 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 0.15 (1936 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 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: 0.145 AC: 22017 AN: 151398 Hom.: 1937 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.0665

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0950

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.145 AC: 22033 AN: 151514 Hom.: 1936 Cov.: 31 AF XY: 0.144 AC XY: 10670 AN XY: 74042

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.0670

Gnomad4 FIN AF: 0.0940

Gnomad4 NFE AF: 0.0950

Gnomad4 OTH AF: 0.147

Alfa AF: 0.127 Hom.: 263

Bravo AF: 0.157

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.9
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4387258; hg19: chr10-29487365;