rs740494

Variant names:

• chr1-230509181-C-G
• rs740494
• ENST00000685406.1:n.241+10215C>G

Variant summary

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

The ENST00000685406.1(ENSG00000282564):​n.241+10215C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 151,950 control chromosomes in the GnomAD database, including 2,926 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 0.19 (2926 hom., cov: 32)
• Consequence: ENSG00000282564 ENST00000685406.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.446
• Publications: 3 publications found

Genes affected

ENSG00000282564 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.412 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
ENSG00000282564	ENST00000685406.1	n.241+10215C>G		intron_variant	Intron 2 of 5
ENSG00000282564	ENST00000689608.2	n.329+10215C>G		intron_variant	Intron 2 of 3
ENSG00000282564	ENST00000692577.3	n.318+10215C>G		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28268 AN: 151832 Hom.: 2931 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.149

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.186 AC: 28255 AN: 151950 Hom.: 2926 Cov.: 32 AF XY: 0.188 AC XY: 13993 AN XY: 74294

African (AFR) AF: 0.127 AC: 5245 AN: 41452

American (AMR) AF: 0.149 AC: 2278 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3466

East Asian (EAS) AF: 0.224 AC: 1155 AN: 5156

South Asian (SAS) AF: 0.427 AC: 2052 AN: 4802

European-Finnish (FIN) AF: 0.169 AC: 1787 AN: 10560

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14512 AN: 67924

Other (OTH) AF: 0.188 AC: 396 AN: 2110

Alfa AF: 0.193 Hom.: 361

Bravo AF: 0.173

Asia WGS AF: 0.323 AC: 1127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.2
DANN	Benign	0.65
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs740494; hg19: chr1-230644927;