rs3858145

Variant names:

• chr10-68252081-A-G
• rs3858145

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 0.332 in 152,016 control chromosomes in the GnomAD database, including 8,917 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 0.33 (8917 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0280
• Publications: 43 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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: 0.332 AC: 50425 AN: 151898 Hom.: 8902 Cov.: 32

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.319

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.332 AC: 50478 AN: 152016 Hom.: 8917 Cov.: 32 AF XY: 0.338 AC XY: 25117 AN XY: 74318

African (AFR) AF: 0.424 AC: 17576 AN: 41442

American (AMR) AF: 0.380 AC: 5796 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1101 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1775 AN: 5162

South Asian (SAS) AF: 0.367 AC: 1769 AN: 4818

European-Finnish (FIN) AF: 0.319 AC: 3368 AN: 10570

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17989 AN: 67976

Other (OTH) AF: 0.301 AC: 636 AN: 2112

Alfa AF: 0.288 Hom.: 31516

Bravo AF: 0.344

Asia WGS AF: 0.322 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		-0.028

Splicing

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

Other links and lift over

dbSNP: rs3858145; hg19: chr10-70011838;