ENST00000672708.1:n.74-1300T>G

Variant names:

• chr10-117583973-T-G
• rs703363
• ENST00000672708.1:n.74-1300T>G

Variant summary

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

The ENST00000672708.1(ENSG00000288172):​n.74-1300T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,218 control chromosomes in the GnomAD database, including 44,034 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 0.76 (44034 hom., cov: 34)
• Consequence: ENSG00000288172 ENST00000672708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.492
• Publications: 1 publications found

Genes affected

ENSG00000288172 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.807 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
ENSG00000288172	ENST00000672708.1	n.74-1300T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114823 AN: 152100 Hom.: 43977 Cov.: 34

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.787

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.755 AC: 114944 AN: 152218 Hom.: 44034 Cov.: 34 AF XY: 0.754 AC XY: 56149 AN XY: 74422

African (AFR) AF: 0.638 AC: 26472 AN: 41520

American (AMR) AF: 0.818 AC: 12523 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.787 AC: 2733 AN: 3472

East Asian (EAS) AF: 0.756 AC: 3909 AN: 5168

South Asian (SAS) AF: 0.638 AC: 3081 AN: 4828

European-Finnish (FIN) AF: 0.804 AC: 8517 AN: 10588

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55049 AN: 68024

Other (OTH) AF: 0.801 AC: 1691 AN: 2112

Alfa AF: 0.788 Hom.: 25843

Bravo AF: 0.755

Asia WGS AF: 0.718 AC: 2497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.7
DANN	Benign	0.49
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs703363; hg19: chr10-119343484;