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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671601.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286469	ENST00000671601.1		n.146+3314T>G		intron	N/A
	ENSG00000286469	ENST00000785058.1		n.134+3314T>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10507679;

hg19: chr13-63145579;