rs10493450

Variant names:

• chr1-68807756-A-T
• rs10493450
• ENST00000643361.1:n.419-56068A>T

Variant summary

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

The ENST00000643361.1(ENSG00000285407):​n.419-56068A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,156 control chromosomes in the GnomAD database, including 1,505 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 (1505 hom., cov: 32)
• Consequence: ENSG00000285407 ENST00000643361.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0950
• Publications: 2 publications found

Genes affected

ENSG00000285407 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.185 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
ENSG00000285407	ENST00000643361.1	n.419-56068A>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19699 AN: 152038 Hom.: 1502 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.0472

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.130 AC: 19721 AN: 152156 Hom.: 1505 Cov.: 32 AF XY: 0.126 AC XY: 9355 AN XY: 74396

African (AFR) AF: 0.176 AC: 7306 AN: 41486

American (AMR) AF: 0.191 AC: 2918 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 481 AN: 3472

East Asian (EAS) AF: 0.0470 AC: 243 AN: 5174

South Asian (SAS) AF: 0.0627 AC: 302 AN: 4818

European-Finnish (FIN) AF: 0.0856 AC: 908 AN: 10606

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7150 AN: 68000

Other (OTH) AF: 0.137 AC: 290 AN: 2114

Alfa AF: 0.124 Hom.: 191

Bravo AF: 0.144

Asia WGS AF: 0.0670 AC: 233 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.2
DANN	Benign	0.64
PhyloP100		0.095

Splicing

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

Other links and lift over

dbSNP: rs10493450; hg19: chr1-69273439;