rs10491557

Variant names:

• chr9-19497272-G-A
• rs10491557
• XR_007061430.1:n.556+9710G>A

Variant summary

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

The XR_929510.4(LOC105375988):​n.412+9710G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0349 in 152,222 control chromosomes in the GnomAD database, including 194 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 0.035 (194 hom., cov: 32)
• Consequence: LOC105375988 XR_929510.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 0 publications found

Genes affected

LOC105375988 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 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: 0.0349 AC: 5307 AN: 152104 Hom.: 196 Cov.: 32

Gnomad AFR AF: 0.0421

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0258

Gnomad ASJ AF: 0.0829

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0171

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0349 AC: 5305 AN: 152222 Hom.: 194 Cov.: 32 AF XY: 0.0375 AC XY: 2793 AN XY: 74442

African (AFR) AF: 0.0422 AC: 1752 AN: 41524

American (AMR) AF: 0.0258 AC: 394 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0829 AC: 288 AN: 3472

East Asian (EAS) AF: 0.139 AC: 718 AN: 5182

South Asian (SAS) AF: 0.148 AC: 714 AN: 4816

European-Finnish (FIN) AF: 0.0139 AC: 148 AN: 10616

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0171 AC: 1166 AN: 68014

Other (OTH) AF: 0.0478 AC: 101 AN: 2114

Alfa AF: 0.0244 Hom.: 6

Bravo AF: 0.0338

Asia WGS AF: 0.126 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.070
DANN	Benign	0.53
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10491557; hg19: chr9-19497270;