rs2163379

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC112268022 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268022	XR_002956694.2	n.8119T>G		non_coding_transcript_exon_variant	1/2

Ensembl

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

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

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.756

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.584

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.648

Alfa AF: 0.612 Hom.: 36692

Bravo AF: 0.653

Asia WGS AF: 0.603 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2163379; hg19: chr8-10732050;