rs10105606

Variant names:

• chr8-19970337-C-A
• rs10105606

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 0.41 in 151,958 control chromosomes in the GnomAD database, including 14,716 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 0.41 (14716 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 43 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 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: 0.410 AC: 62284 AN: 151840 Hom.: 14679 Cov.: 31

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.410 AC: 62367 AN: 151958 Hom.: 14716 Cov.: 31 AF XY: 0.404 AC XY: 30014 AN XY: 74288

African (AFR) AF: 0.657 AC: 27221 AN: 41420

American (AMR) AF: 0.338 AC: 5164 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1568 AN: 3470

East Asian (EAS) AF: 0.207 AC: 1068 AN: 5168

South Asian (SAS) AF: 0.282 AC: 1354 AN: 4808

European-Finnish (FIN) AF: 0.277 AC: 2923 AN: 10550

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21710 AN: 67968

Other (OTH) AF: 0.390 AC: 822 AN: 2106

Alfa AF: 0.348 Hom.: 42577

Bravo AF: 0.424

Asia WGS AF: 0.292 AC: 1017 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	0.53
DANN	Benign	0.30
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10105606; hg19: chr8-19827848;