ENST00000804402.1:n.194-62G>A

Variant names:

• chr10-114047257-C-T
• rs3813720
• ENST00000804402.1:n.194-62G>A

Variant summary

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

The ENST00000804402.1(ENSG00000304538):​n.194-62G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.622 in 149,880 control chromosomes in the GnomAD database, including 29,298 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 0.62 (29298 hom., cov: 27)
• Consequence: ENSG00000304538 ENST00000804402.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800
• Publications: 6 publications found

Genes affected

ENSG00000304538 (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 (EAS) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902554	XR_007062383.1	n.194-62G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304538	ENST00000804402.1	n.194-62G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.622 AC: 93124 AN: 149770 Hom.: 29264 Cov.: 27

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.545

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.622 AC: 93208 AN: 149880 Hom.: 29298 Cov.: 27 AF XY: 0.629 AC XY: 45894 AN XY: 72918

African (AFR) AF: 0.532 AC: 21615 AN: 40620

American (AMR) AF: 0.691 AC: 10407 AN: 15050

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1925 AN: 3462

East Asian (EAS) AF: 0.759 AC: 3874 AN: 5104

South Asian (SAS) AF: 0.688 AC: 3284 AN: 4774

European-Finnish (FIN) AF: 0.729 AC: 7183 AN: 9848

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.634 AC: 42988 AN: 67754

Other (OTH) AF: 0.603 AC: 1251 AN: 2074

Alfa AF: 0.629 Hom.: 50736

Bravo AF: 0.611

Asia WGS AF: 0.689 AC: 2393 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	4.7
DANN	Benign	0.76
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs3813720; hg19: chr10-115807016;