rs10220851

Positions:

• chr15-68012869-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;