rs10458561

Variant names:

• chr1-70455490-G-A
• rs10458561
• ENST00000819442.1:n.165-2641G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-70455490-G-A
• chr1-70455490-G-T

Variant summary

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

The ENST00000819442.1(ENSG00000306574):​n.165-2641G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,898 control chromosomes in the GnomAD database, including 5,746 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 0.27 (5746 hom., cov: 32)
• Consequence: ENSG00000306574 ENST00000819442.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110
• Publications: 16 publications found

Genes affected

ENSG00000306574 (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 (NFE) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378793	XR_947499.2	n.411-2641G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306574	ENST00000819442.1	n.165-2641G>A		intron_variant	Intron 1 of 3
ENSG00000306574	ENST00000819444.1	n.180-2641G>A		intron_variant	Intron 1 of 2
ENSG00000306574	ENST00000819445.1	n.171-2641G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40444 AN: 151780 Hom.: 5747 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.266 AC: 40440 AN: 151898 Hom.: 5746 Cov.: 32 AF XY: 0.265 AC XY: 19653 AN XY: 74238

African (AFR) AF: 0.188 AC: 7773 AN: 41404

American (AMR) AF: 0.224 AC: 3420 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 996 AN: 3468

East Asian (EAS) AF: 0.120 AC: 620 AN: 5162

South Asian (SAS) AF: 0.203 AC: 977 AN: 4812

European-Finnish (FIN) AF: 0.350 AC: 3679 AN: 10526

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.325 AC: 22069 AN: 67962

Other (OTH) AF: 0.265 AC: 559 AN: 2112

Alfa AF: 0.286 Hom.: 12281

Bravo AF: 0.252

Asia WGS AF: 0.133 AC: 463 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	2.3
DANN	Benign	0.71
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10458561; hg19: chr1-70921173;