rs10995439

chr10-63107152-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 0.402 in 152,126 control chromosomes in the GnomAD database, including 15,036 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 0.40 (15036 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.552 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: 0.403 AC: 61226 AN: 152008 Hom.: 15043 Cov.: 32

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.402 AC: 61204 AN: 152126 Hom.: 15036 Cov.: 32 AF XY: 0.401 AC XY: 29854 AN XY: 74376

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.612

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.407

Alfa AF: 0.494 Hom.: 4147

Bravo AF: 0.371

Asia WGS AF: 0.309 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10995439; hg19: chr10-64866912;