chr8-69360962-G-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901958	XR_007060956.1	n.2926G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299218	ENST00000761642.1	n.62-3513C>T		intron_variant	Intron 1 of 2
ENSG00000299233	ENST00000761726.1	n.342+2312G>A		intron_variant	Intron 2 of 2
ENSG00000299233	ENST00000761727.1	n.554+2302G>A		intron_variant	Intron 2 of 2

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 v4.3

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;