rs2163379

Variant names:

• chr8-10874540-A-C
• rs2163379
• XR_002956694.2:n.8119T>G

Your query was ambiguous. Multiple possible variants found:

• chr8-10874540-A-C
• chr8-10874540-A-G
• chr8-10874540-A-T

Variant summary

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

The XR_002956694.2(LOC112268022):​n.8119T>G 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 0.651 in 152,014 control chromosomes in the GnomAD database, including 33,471 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 0.65 (33471 hom., cov: 31)
• Consequence: LOC112268022 XR_002956694.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 9 publications found

Genes affected

LOC112268022 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.816 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98929 AN: 151896 Hom.: 33418 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.651 AC: 99035 AN: 152014 Hom.: 33471 Cov.: 31 AF XY: 0.642 AC XY: 47693 AN XY: 74292

African (AFR) AF: 0.823 AC: 34172 AN: 41498

American (AMR) AF: 0.505 AC: 7713 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2626 AN: 3472

East Asian (EAS) AF: 0.504 AC: 2597 AN: 5154

South Asian (SAS) AF: 0.584 AC: 2804 AN: 4798

European-Finnish (FIN) AF: 0.519 AC: 5475 AN: 10556

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41723 AN: 67946

Other (OTH) AF: 0.648 AC: 1365 AN: 2106

Alfa AF: 0.620 Hom.: 53316

Bravo AF: 0.653

Asia WGS AF: 0.603 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.8
DANN	Benign	0.35
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs2163379; hg19: chr8-10732050;