rs2959025

Positions:

• chr8-104467952-A-G
• chr8-104467952-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_928507.3(LOC105375691):​n.219-1775A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,192 control chromosomes in the GnomAD database, including 6,685 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 0.28 (6685 hom., cov: 32)
• Consequence: LOC105375691 XR_928507.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

Genes affected

LOC105375691 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375691	XR_928507.3	n.219-1775A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42191 AN: 152076 Hom.: 6689 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.277 AC: 42209 AN: 152192 Hom.: 6685 Cov.: 32 AF XY: 0.279 AC XY: 20758 AN XY: 74400

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.293

Alfa AF: 0.343 Hom.: 13212

Bravo AF: 0.265

Asia WGS AF: 0.347 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.3
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2959025; hg19: chr8-105480180;