XR_007060956.1:n.2926G>A

Variant names:

• chr8-69360962-G-A
• rs955436
• XR_007060956.1:n.2926G>A

Variant summary

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

The XR_007060956.1(LOC124901958):​n.2926G>A 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 0.421 in 151,986 control chromosomes in the GnomAD database, including 13,644 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 0.42 (13644 hom., cov: 32)
• Consequence: LOC124901958 XR_007060956.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797
• Publications: 3 publications found

Genes affected

LOC124901958 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000761642.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000299218	ENST00000761642.1		n.62-3513C>T		intron	N/A
	ENSG00000299233	ENST00000761726.1		n.342+2312G>A		intron	N/A
	ENSG00000299233	ENST00000761727.1		n.554+2302G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63879 AN: 151868 Hom.: 13622 Cov.: 32

Gnomad AFR AF: 0.458

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.357

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.421 AC: 63939 AN: 151986 Hom.: 13644 Cov.: 32 AF XY: 0.428 AC XY: 31774 AN XY: 74292

African (AFR) AF: 0.458 AC: 18976 AN: 41430

American (AMR) AF: 0.426 AC: 6511 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.357 AC: 1238 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2489 AN: 5162

South Asian (SAS) AF: 0.389 AC: 1873 AN: 4820

European-Finnish (FIN) AF: 0.482 AC: 5087 AN: 10548

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26541 AN: 67964

Other (OTH) AF: 0.373 AC: 789 AN: 2116

Alfa AF: 0.394 Hom.: 15582

Bravo AF: 0.414

Asia WGS AF: 0.432 AC: 1507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.27
DANN	Benign	0.33
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs955436; hg19: chr8-70273197;