rs3814570

Positions:

• chr10-112948751-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;