rs10458561

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_947499.2(LOC105378793):​n.411-2641G>A variant causes a intron, non coding transcript 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: LOC105378793 XR_947499.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

Genes affected

LOC105378793 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105378793	XR_947499.2	n.411-2641G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.265

Alfa AF: 0.294 Hom.: 8270

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10458561; hg19: chr1-70921173;