XR_007061731.1:n.5250T>C

Variant names:

• chr9-110621718-T-C
• rs10980495
• XR_007061731.1:n.5250T>C

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.169 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: 0.157 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

African (AFR) AF: 0.151 AC: 6260 AN: 41528

American (AMR) AF: 0.129 AC: 1978 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 550 AN: 3468

East Asian (EAS) AF: 0.0659 AC: 342 AN: 5186

South Asian (SAS) AF: 0.133 AC: 639 AN: 4818

European-Finnish (FIN) AF: 0.181 AC: 1916 AN: 10574

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.171 AC: 11650 AN: 67988

Other (OTH) AF: 0.159 AC: 334 AN: 2106

Alfa AF: 0.164 Hom.: 383

Bravo AF: 0.152

Asia WGS AF: 0.0960 AC: 336 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.49
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs10980495; hg19: chr9-113383998;