9-110618613-C-T

Variant names:

• chr9-110618613-C-T
• rs10448267
• XR_001746891.2:n.3254C>T

Variant summary

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

The XR_001746891.2(LOC105376218):​n.3254C>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 0.172 in 151,894 control chromosomes in the GnomAD database, including 2,335 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 0.17 (2335 hom., cov: 32)
• Consequence: LOC105376218 XR_001746891.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.485
• Publications: 3 publications found

Genes affected

LOC105376218 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26067 AN: 151776 Hom.: 2332 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.0657

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.172 AC: 26086 AN: 151894 Hom.: 2335 Cov.: 32 AF XY: 0.170 AC XY: 12619 AN XY: 74242

African (AFR) AF: 0.203 AC: 8403 AN: 41440

American (AMR) AF: 0.133 AC: 2031 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 549 AN: 3470

East Asian (EAS) AF: 0.0658 AC: 341 AN: 5180

South Asian (SAS) AF: 0.133 AC: 639 AN: 4804

European-Finnish (FIN) AF: 0.182 AC: 1929 AN: 10582

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11641 AN: 67880

Other (OTH) AF: 0.169 AC: 355 AN: 2106

Alfa AF: 0.154 Hom.: 1129

Bravo AF: 0.169

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.0
DANN	Benign	0.68
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10448267; hg19: chr9-113380893;