10-63107152-G-A

Variant names:

• chr10-63107152-G-A
• rs10995439

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 0.402 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.139 AC: 5752 AN: 41518

American (AMR) AF: 0.314 AC: 4791 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1804 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1421 AN: 5166

South Asian (SAS) AF: 0.368 AC: 1775 AN: 4824

European-Finnish (FIN) AF: 0.612 AC: 6468 AN: 10566

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.557 AC: 37850 AN: 67996

Other (OTH) AF: 0.407 AC: 858 AN: 2110

Alfa AF: 0.490 Hom.: 30429

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
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs10995439; hg19: chr10-64866912;