ENST00000810814.1:n.102-20847T>C

Variant names:

• chr1-77261295-A-G
• rs10518441
• ENST00000810814.1:n.102-20847T>C

Variant summary

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

The ENST00000810814.1(ENSG00000305415):​n.102-20847T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,212 control chromosomes in the GnomAD database, including 1,639 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 0.13 (1639 hom., cov: 32)
• Consequence: ENSG00000305415 ENST00000810814.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 3 publications found

Genes affected

ENSG00000305415 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.183 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
ENSG00000305415	ENST00000810814.1	n.102-20847T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20241 AN: 152094 Hom.: 1637 Cov.: 32

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.133 AC: 20252 AN: 152212 Hom.: 1639 Cov.: 32 AF XY: 0.133 AC XY: 9925 AN XY: 74412

African (AFR) AF: 0.0695 AC: 2886 AN: 41550

American (AMR) AF: 0.189 AC: 2894 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 554 AN: 3468

East Asian (EAS) AF: 0.0467 AC: 242 AN: 5186

South Asian (SAS) AF: 0.184 AC: 887 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1215 AN: 10592

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11093 AN: 67990

Other (OTH) AF: 0.119 AC: 251 AN: 2106

Alfa AF: 0.157 Hom.: 1190

Bravo AF: 0.135

Asia WGS AF: 0.106 AC: 370 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10518441; hg19: chr1-77726980;