rs1505863

Variant names:

• chr4-138690148-C-T
• rs1505863

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 0.252 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.477 AC: 19783 AN: 41454

American (AMR) AF: 0.242 AC: 3697 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3470

East Asian (EAS) AF: 0.608 AC: 3133 AN: 5156

South Asian (SAS) AF: 0.318 AC: 1525 AN: 4798

European-Finnish (FIN) AF: 0.103 AC: 1089 AN: 10582

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.119 AC: 8095 AN: 67974

Other (OTH) AF: 0.226 AC: 476 AN: 2104

Alfa AF: 0.282 Hom.: 3433

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
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs1505863; hg19: chr4-139611302;