rs10493900

Variant names:

• chr1-98179657-A-G
• rs10493900
• XR_007066241.1:n.126-102703A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007066241.1(LOC124900404):​n.126-102703A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 151,850 control chromosomes in the GnomAD database, including 2,643 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 0.18 (2643 hom., cov: 32)
• Consequence: LOC124900404 XR_007066241.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0500
• Publications: 3 publications found

Genes affected

LOC124900404 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900404	XR_007066241.1	n.126-102703A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27080 AN: 151730 Hom.: 2638 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0589

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.178 AC: 27099 AN: 151850 Hom.: 2643 Cov.: 32 AF XY: 0.179 AC XY: 13244 AN XY: 74184

African (AFR) AF: 0.175 AC: 7269 AN: 41446

American (AMR) AF: 0.248 AC: 3767 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 920 AN: 3462

East Asian (EAS) AF: 0.0590 AC: 303 AN: 5134

South Asian (SAS) AF: 0.120 AC: 580 AN: 4814

European-Finnish (FIN) AF: 0.176 AC: 1862 AN: 10590

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11731 AN: 67880

Other (OTH) AF: 0.212 AC: 448 AN: 2112

Alfa AF: 0.181 Hom.: 8222

Bravo AF: 0.185

Asia WGS AF: 0.104 AC: 361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		0.050

Splicing

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

Other links and lift over

dbSNP: rs10493900; hg19: chr1-98645213;