8-56434567-T-C

Variant names:

• chr8-56434567-T-C
• rs2196586
• ENST00000756461.1:n.87-31T>C

Variant summary

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

The ENST00000756461.1(ENSG00000298562):​n.87-31T>C variant causes a intron 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: ENSG00000298562 ENST00000756461.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.567
• Publications: 3 publications found

Genes affected

ENSG00000298562 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375849	XR_928910.2	n.54+262A>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298562	ENST00000756461.1	n.87-31T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.739 AC: 30575 AN: 41364

American (AMR) AF: 0.798 AC: 12175 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.801 AC: 2778 AN: 3470

East Asian (EAS) AF: 0.869 AC: 4480 AN: 5154

South Asian (SAS) AF: 0.868 AC: 4169 AN: 4802

European-Finnish (FIN) AF: 0.804 AC: 8488 AN: 10558

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.765 AC: 51989 AN: 67966

Other (OTH) AF: 0.777 AC: 1639 AN: 2110

Alfa AF: 0.769 Hom.: 8636

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs2196586; hg19: chr8-57347126;