10-31596296-G-C

Variant names:

• chr10-31596296-G-C
• rs7092560
• ENST00000829893.1:n.310+7467C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000829893.1(ENSG00000307931):​n.310+7467C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 151,914 control chromosomes in the GnomAD database, including 43,424 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 0.75 (43424 hom., cov: 32)
• Consequence: ENSG00000307931 ENST00000829893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209
• Publications: 1 publications found

Genes affected

ENSG00000307931 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.907 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
ENSG00000307931	ENST00000829893.1	n.310+7467C>G		intron_variant	Intron 1 of 1
ENSG00000223834	ENST00000830032.1	n.247-6825G>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113450 AN: 151792 Hom.: 43357 Cov.: 32

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.647

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.748 AC: 113577 AN: 151914 Hom.: 43424 Cov.: 32 AF XY: 0.740 AC XY: 54925 AN XY: 74218

African (AFR) AF: 0.915 AC: 37966 AN: 41512

American (AMR) AF: 0.720 AC: 10988 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2454 AN: 3468

East Asian (EAS) AF: 0.523 AC: 2699 AN: 5162

South Asian (SAS) AF: 0.582 AC: 2802 AN: 4816

European-Finnish (FIN) AF: 0.631 AC: 6648 AN: 10530

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.703 AC: 47714 AN: 67866

Other (OTH) AF: 0.712 AC: 1502 AN: 2110

Alfa AF: 0.600 Hom.: 1548

Bravo AF: 0.768

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.83
DANN	Benign	0.37
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7092560; hg19: chr10-31885224;