XR_930260.2:n.201-1521T>C

Variant names:

• chr9-114560262-A-G
• rs10817638
• XR_930260.2:n.201-1521T>C

Variant summary

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

The XR_930260.2(LOC105376229):​n.201-1521T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,116 control chromosomes in the GnomAD database, including 10,519 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 0.37 (10519 hom., cov: 32)
• Consequence: LOC105376229 XR_930260.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.34
• Publications: 13 publications found

Genes affected

LOC105376229 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376229	XR_930260.2	n.201-1521T>C		intron_variant	Intron 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56245 AN: 151998 Hom.: 10511 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.370 AC: 56268 AN: 152116 Hom.: 10519 Cov.: 32 AF XY: 0.370 AC XY: 27504 AN XY: 74338

African (AFR) AF: 0.371 AC: 15371 AN: 41480

American (AMR) AF: 0.460 AC: 7028 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3468

East Asian (EAS) AF: 0.404 AC: 2084 AN: 5162

South Asian (SAS) AF: 0.367 AC: 1770 AN: 4820

European-Finnish (FIN) AF: 0.329 AC: 3485 AN: 10590

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.356 AC: 24220 AN: 68008

Other (OTH) AF: 0.368 AC: 778 AN: 2112

Alfa AF: 0.367 Hom.: 31374

Bravo AF: 0.381

Asia WGS AF: 0.366 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.51
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs10817638; hg19: chr9-117322542;