rs10883617

Positions:

• chr10-101353278-T-C

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 0.279 in 152,106 control chromosomes in the GnomAD database, including 6,540 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 0.28 (6540 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.353 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: 0.279 AC: 42353 AN: 151988 Hom.: 6534 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.279 AC: 42378 AN: 152106 Hom.: 6540 Cov.: 32 AF XY: 0.275 AC XY: 20481 AN XY: 74352

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.284

Alfa AF: 0.343 Hom.: 12518

Bravo AF: 0.270

Asia WGS AF: 0.174 AC: 606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10883617; hg19: chr10-103113035;