chr10-47314603-A-G

Variant names:

• chr10-47314603-A-G
• rs7093975

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 0.689 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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.585 AC: 24275 AN: 41504

American (AMR) AF: 0.746 AC: 11422 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2480 AN: 3472

East Asian (EAS) AF: 0.750 AC: 3881 AN: 5172

South Asian (SAS) AF: 0.605 AC: 2917 AN: 4820

European-Finnish (FIN) AF: 0.752 AC: 7985 AN: 10612

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.727 AC: 49428 AN: 68004

Other (OTH) AF: 0.698 AC: 1474 AN: 2112

Alfa AF: 0.714 Hom.: 61244

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
PhyloP100		0.071

Splicing

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

Other links and lift over

dbSNP: rs7093975; hg19: chr10-48424759;