chr1-98179657-A-G

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;