rs9421758

Variant names:

• chr10-47205758-C-A
• rs9421758
• XR_945937.3:n.104-1603C>A

Variant summary

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

The XR_945937.3(LOC105378291):​n.104-1603C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,040 control chromosomes in the GnomAD database, including 5,274 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 0.24 (5274 hom., cov: 33)
• Consequence: LOC105378291 XR_945937.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.302
• Publications: 3 publications found

Genes affected

LOC105378291 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378291	XR_945937.3	n.104-1603C>A		intron_variant	Intron 1 of 4

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35762 AN: 151924 Hom.: 5268 Cov.: 33

Gnomad AFR AF: 0.0638

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.235 AC: 35766 AN: 152040 Hom.: 5274 Cov.: 33 AF XY: 0.242 AC XY: 17984 AN XY: 74284

African (AFR) AF: 0.0637 AC: 2644 AN: 41502

American (AMR) AF: 0.335 AC: 5117 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3470

East Asian (EAS) AF: 0.142 AC: 733 AN: 5168

South Asian (SAS) AF: 0.407 AC: 1957 AN: 4808

European-Finnish (FIN) AF: 0.362 AC: 3815 AN: 10532

Middle Eastern (MID) AF: 0.272 AC: 79 AN: 290

European-Non Finnish (NFE) AF: 0.288 AC: 19560 AN: 67966

Other (OTH) AF: 0.248 AC: 523 AN: 2112

Alfa AF: 0.275 Hom.: 8744

Bravo AF: 0.222

Asia WGS AF: 0.299 AC: 1038 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.8
DANN	Benign	0.68
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9421758; hg19: chr10-48533604;