10-31586041-A-G

Variant names:

• chr10-31586041-A-G
• rs10763867
• ENST00000830134.1:n.1340T>C

Variant summary

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

The ENST00000830134.1(ENSG00000307972):​n.1340T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,110 control chromosomes in the GnomAD database, including 20,087 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 0.47 (20087 hom., cov: 32)
• Consequence: ENSG00000307972 ENST00000830134.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148
• Publications: 5 publications found

Genes affected

ENSG00000307972 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.63 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
ENSG00000307972	ENST00000830134.1	n.1340T>C		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000307931	ENST00000829893.1	n.310+17722T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71922 AN: 151992 Hom.: 20072 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.533

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.473 AC: 71949 AN: 152110 Hom.: 20087 Cov.: 32 AF XY: 0.467 AC XY: 34752 AN XY: 74344

African (AFR) AF: 0.166 AC: 6893 AN: 41524

American (AMR) AF: 0.588 AC: 8994 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.533 AC: 1848 AN: 3470

East Asian (EAS) AF: 0.395 AC: 2041 AN: 5164

South Asian (SAS) AF: 0.433 AC: 2087 AN: 4822

European-Finnish (FIN) AF: 0.493 AC: 5204 AN: 10550

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.635 AC: 43179 AN: 67978

Other (OTH) AF: 0.491 AC: 1036 AN: 2112

Alfa AF: 0.586 Hom.: 116313

Bravo AF: 0.472

Asia WGS AF: 0.374 AC: 1305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.28
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10763867; hg19: chr10-31874969;