rs955436

chr8-69360962-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC124901958 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124901958	XR_007060956.1	n.2926G>A		non_coding_transcript_exon_variant	2/2

Ensembl

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

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

Gnomad4 AFR AF: 0.458

Gnomad4 AMR AF: 0.426

Gnomad4 ASJ AF: 0.357

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.482

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.373

Alfa AF: 0.389 Hom.: 11779

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs955436; hg19: chr8-70273197;