rs2196586

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756461.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298562	ENST00000756461.1		n.87-31T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2196586;

hg19: chr8-57347126;