rs10502887

Variant names:

• chr18-47653512-A-G
• rs10502887

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 0.491 in 152,028 control chromosomes in the GnomAD database, including 19,405 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 0.49 (19405 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.566 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: 0.491 AC: 74645 AN: 151908 Hom.: 19403 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.453

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.491 AC: 74670 AN: 152028 Hom.: 19405 Cov.: 32 AF XY: 0.488 AC XY: 36250 AN XY: 74302

African (AFR) AF: 0.328 AC: 13596 AN: 41462

American (AMR) AF: 0.569 AC: 8686 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2434 AN: 3470

East Asian (EAS) AF: 0.393 AC: 2027 AN: 5154

South Asian (SAS) AF: 0.513 AC: 2480 AN: 4830

European-Finnish (FIN) AF: 0.453 AC: 4784 AN: 10556

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38789 AN: 67964

Other (OTH) AF: 0.573 AC: 1209 AN: 2110

Alfa AF: 0.556 Hom.: 67060

Bravo AF: 0.498

Asia WGS AF: 0.424 AC: 1479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.2
DANN	Benign	0.81
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs10502887; hg19: chr18-45179883;