rs10220851

Variant names:

• chr15-68012869-G-A
• rs10220851

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 0.443 in 151,880 control chromosomes in the GnomAD database, including 15,387 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 0.44 (15387 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.369

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.443 AC: 67289 AN: 151762 Hom.: 15384 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.443 AC: 67316 AN: 151880 Hom.: 15387 Cov.: 31 AF XY: 0.447 AC XY: 33201 AN XY: 74222

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.499

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.441

Alfa AF: 0.450 Hom.: 2014

Bravo AF: 0.443

Asia WGS AF: 0.627 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.8
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10220851; hg19: chr15-68305207;