rs1502856

Positions:

• chr1-50406175-G-A
• chr1-50406175-G-C
• chr1-50406175-G-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 0.509 in 152,090 control chromosomes in the GnomAD database, including 20,987 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 0.51 (20987 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.804 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: 0.510 AC: 77443 AN: 151972 Hom.: 20972 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.589

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.509 AC: 77470 AN: 152090 Hom.: 20987 Cov.: 33 AF XY: 0.522 AC XY: 38835 AN XY: 74358

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.825

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.482

Alfa AF: 0.510 Hom.: 31166

Bravo AF: 0.495

Asia WGS AF: 0.666 AC: 2314 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1502856; hg19: chr1-50871847;