rs2196586

Positions:

• chr8-56434567-T-C

Variant summary

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

The XR_928910.2(LOC105375849):​n.54+262A>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 0.772 in 151,880 control chromosomes in the GnomAD database, including 45,395 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 0.77 (45395 hom., cov: 29)
• Consequence: LOC105375849 XR_928910.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567

Genes affected

LOC105375849 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.848 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375849	XR_928910.2	n.54+262A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117185 AN: 151762 Hom.: 45366 Cov.: 29

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.869

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.772 AC: 117268 AN: 151880 Hom.: 45395 Cov.: 29 AF XY: 0.775 AC XY: 57476 AN XY: 74206

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.869

Gnomad4 SAS AF: 0.868

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.777

Alfa AF: 0.770 Hom.: 8416

Bravo AF: 0.769

Asia WGS AF: 0.873 AC: 3036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2196586; hg19: chr8-57347126;