rs3814614

Variant names:

• chr10-86368524-A-G
• rs3814614

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 0.603 in 151,914 control chromosomes in the GnomAD database, including 29,537 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 0.60 (29537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.817 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: 0.603 AC: 91511 AN: 151796 Hom.: 29501 Cov.: 32

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.603 AC: 91591 AN: 151914 Hom.: 29537 Cov.: 32 AF XY: 0.601 AC XY: 44601 AN XY: 74230

African (AFR) AF: 0.824 AC: 34171 AN: 41464

American (AMR) AF: 0.378 AC: 5767 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2140 AN: 3466

East Asian (EAS) AF: 0.756 AC: 3907 AN: 5168

South Asian (SAS) AF: 0.742 AC: 3564 AN: 4806

European-Finnish (FIN) AF: 0.515 AC: 5427 AN: 10532

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.513 AC: 34815 AN: 67926

Other (OTH) AF: 0.545 AC: 1149 AN: 2108

Alfa AF: 0.535 Hom.: 38054

Bravo AF: 0.594

Asia WGS AF: 0.729 AC: 2535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.50
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs3814614; hg19: chr10-88128281;