rs10980495

chr9-110621718-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007061731.1(LOC105376218):n.5250T>C 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 0.157 in 152,162 control chromosomes in the GnomAD database, including 1,956 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 (1956 hom., cov: 32)
• Consequence: LOC105376218 XR_007061731.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

Genes affected

LOC105376218 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376218	XR_007061731.1	n.5250T>C		non_coding_transcript_exon_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23852 AN: 152044 Hom.: 1955 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.0658

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.157 AC: 23863 AN: 152162 Hom.: 1956 Cov.: 32 AF XY: 0.156 AC XY: 11585 AN XY: 74388

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.159

Gnomad4 EAS AF: 0.0659

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.181

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.159

Alfa AF: 0.164 Hom.: 374

Bravo AF: 0.152

Asia WGS AF: 0.0960 AC: 336 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.3
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10980495; hg19: chr9-113383998;