chr9-101841564-A-G

Variant names:

• chr9-101841564-A-G
• rs10512291
• XR_930187.3:n.134+7007T>C

Variant summary

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

The XR_930187.3(LOC105376187):​n.134+7007T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,112 control chromosomes in the GnomAD database, including 2,525 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 0.16 (2525 hom., cov: 32)
• Consequence: LOC105376187 XR_930187.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.567
• Publications: 2 publications found

Genes affected

LOC105376187 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376187	XR_930187.3	n.134+7007T>C		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25031 AN: 151994 Hom.: 2526 Cov.: 32

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.164 AC: 25019 AN: 152112 Hom.: 2525 Cov.: 32 AF XY: 0.163 AC XY: 12122 AN XY: 74340

African (AFR) AF: 0.0424 AC: 1762 AN: 41558

American (AMR) AF: 0.165 AC: 2513 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 756 AN: 3468

East Asian (EAS) AF: 0.144 AC: 744 AN: 5172

South Asian (SAS) AF: 0.144 AC: 693 AN: 4820

European-Finnish (FIN) AF: 0.206 AC: 2175 AN: 10558

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15775 AN: 67964

Other (OTH) AF: 0.189 AC: 399 AN: 2110

Alfa AF: 0.217 Hom.: 2566

Bravo AF: 0.160

Asia WGS AF: 0.137 AC: 475 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.64
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs10512291; hg19: chr9-104603846; COSMIC: COSV60382661;