rs1505863

chr4-138690148-C-T

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 0.252 in 152,034 control chromosomes in the GnomAD database, including 7,059 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 0.25 (7059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.531

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.59 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38218 AN: 151916 Hom.: 7049 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.103

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.119

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.252 AC: 38268 AN: 152034 Hom.: 7059 Cov.: 32 AF XY: 0.253 AC XY: 18822 AN XY: 74300

Gnomad4 AFR AF: 0.477

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.103

Gnomad4 NFE AF: 0.119

Gnomad4 OTH AF: 0.226

Alfa AF: 0.206 Hom.: 734

Bravo AF: 0.273

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.7
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1505863; hg19: chr4-139611302;