chr9-111040905-C-T

Variant names:

• chr9-111040905-C-T
• rs10980705
• XR_007061732.1:n.2313C>T

Variant summary

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

The XR_007061732.1(LOC124902248):​n.2313C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,106 control chromosomes in the GnomAD database, including 3,055 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 (3055 hom., cov: 32)
• Consequence: LOC124902248 XR_007061732.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.35
• Publications: 10 publications found

Genes affected

LOC124902248 (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 (AMR) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902248	XR_007061732.1	n.2313C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27538 AN: 151986 Hom.: 3048 Cov.: 32

Gnomad AFR AF: 0.0490

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.189

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

GnomAD4 genome AF: 0.181 AC: 27556 AN: 152106 Hom.: 3055 Cov.: 32 AF XY: 0.181 AC XY: 13436 AN XY: 74346

African (AFR) AF: 0.0488 AC: 2029 AN: 41536

American (AMR) AF: 0.263 AC: 4022 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3470

East Asian (EAS) AF: 0.250 AC: 1294 AN: 5178

South Asian (SAS) AF: 0.150 AC: 721 AN: 4812

European-Finnish (FIN) AF: 0.194 AC: 2053 AN: 10572

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.237 AC: 16117 AN: 67930

Other (OTH) AF: 0.194 AC: 410 AN: 2112

Alfa AF: 0.226 Hom.: 4652

Bravo AF: 0.182

Asia WGS AF: 0.213 AC: 739 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	0.48
DANN	Benign	0.22
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10980705; hg19: chr9-113803185;