chr10-47314603-A-G

Position:

• chr10-47314603-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.689 in 152,202 control chromosomes in the GnomAD database, including 36,538 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 0.69 (36538 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 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: 0.689 AC: 104816 AN: 152082 Hom.: 36522 Cov.: 34

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.746

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.752

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.727

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.689 AC: 104886 AN: 152202 Hom.: 36538 Cov.: 34 AF XY: 0.691 AC XY: 51381 AN XY: 74400

Gnomad4 AFR AF: 0.585

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.750

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.752

Gnomad4 NFE AF: 0.727

Gnomad4 OTH AF: 0.698

Alfa AF: 0.716 Hom.: 43319

Bravo AF: 0.686

Asia WGS AF: 0.650 AC: 2264 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.5
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7093975; hg19: chr10-48424759;