rs10106587

Variant names:

• chr8-63041520-A-C
• rs10106587

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 0.273 in 152,140 control chromosomes in the GnomAD database, including 5,848 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 0.27 (5848 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.429
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.37 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: 0.273 AC: 41452 AN: 152020 Hom.: 5838 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.273 AC: 41490 AN: 152140 Hom.: 5848 Cov.: 33 AF XY: 0.274 AC XY: 20353 AN XY: 74370

African (AFR) AF: 0.251 AC: 10431 AN: 41512

American (AMR) AF: 0.209 AC: 3196 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3472

East Asian (EAS) AF: 0.140 AC: 725 AN: 5184

South Asian (SAS) AF: 0.384 AC: 1853 AN: 4822

European-Finnish (FIN) AF: 0.346 AC: 3651 AN: 10558

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19979 AN: 67970

Other (OTH) AF: 0.255 AC: 539 AN: 2116

Alfa AF: 0.293 Hom.: 1323

Bravo AF: 0.257

Asia WGS AF: 0.269 AC: 935 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.6
DANN	Benign	0.73
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs10106587; hg19: chr8-63954079;