rs10507679

Variant names:

• chr13-62571446-A-C
• rs10507679
• ENST00000671601.1:n.146+3314T>G

Variant summary

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

The ENST00000671601.1(ENSG00000286469):​n.146+3314T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0927 in 152,112 control chromosomes in the GnomAD database, including 735 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 0.093 (735 hom., cov: 31)
• Consequence: ENSG00000286469 ENST00000671601.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656
• Publications: 0 publications found

Genes affected

ENSG00000286469 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370232	XR_942011.3	n.146+3314T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286469	ENST00000671601.1	n.146+3314T>G		intron_variant	Intron 1 of 2
ENSG00000286469	ENST00000785058.1	n.134+3314T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 14105 AN: 151994 Hom.: 740 Cov.: 31

Gnomad AFR AF: 0.0881

Gnomad AMI AF: 0.136

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0117

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0945

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0854

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0927 AC: 14103 AN: 152112 Hom.: 735 Cov.: 31 AF XY: 0.0954 AC XY: 7094 AN XY: 74344

African (AFR) AF: 0.0879 AC: 3648 AN: 41512

American (AMR) AF: 0.130 AC: 1975 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3462

East Asian (EAS) AF: 0.0118 AC: 61 AN: 5186

South Asian (SAS) AF: 0.119 AC: 573 AN: 4828

European-Finnish (FIN) AF: 0.0945 AC: 1001 AN: 10596

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0854 AC: 5803 AN: 67958

Other (OTH) AF: 0.111 AC: 234 AN: 2114

Alfa AF: 0.0928 Hom.: 1190

Bravo AF: 0.0941

Asia WGS AF: 0.0790 AC: 275 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.79
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs10507679; hg19: chr13-63145579;