rs3814570

Variant names:

• chr10-112948751-C-T
• rs3814570

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.227 in 151,982 control chromosomes in the GnomAD database, including 4,391 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 0.23 (4391 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.96

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 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: 0.227 AC: 34412 AN: 151864 Hom.: 4386 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.0646

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.227 AC: 34434 AN: 151982 Hom.: 4391 Cov.: 31 AF XY: 0.225 AC XY: 16735 AN XY: 74282

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.0650

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.245

Alfa AF: 0.274 Hom.: 7463

Bravo AF: 0.221

Asia WGS AF: 0.172 AC: 597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	15
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3814570; hg19: chr10-114708510;