8-112061867-C-T

Variant names:

• chr8-112061867-C-T
• rs1996720
• ENST00000805473.1:n.374+3782G>A

Variant summary

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

The ENST00000805473.1(ENSG00000304690):​n.374+3782G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 151,952 control chromosomes in the GnomAD database, including 15,704 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 0.41 (15704 hom., cov: 32)
• Consequence: ENSG00000304690 ENST00000805473.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 3 publications found

Genes affected

ENSG00000304690 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000805473.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304690	ENST00000805473.1		n.374+3782G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62752 AN: 151834 Hom.: 15675 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.379

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.413 AC: 62828 AN: 151952 Hom.: 15704 Cov.: 32 AF XY: 0.410 AC XY: 30486 AN XY: 74276

African (AFR) AF: 0.710 AC: 29447 AN: 41476

American (AMR) AF: 0.340 AC: 5182 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1273 AN: 3470

East Asian (EAS) AF: 0.378 AC: 1942 AN: 5142

South Asian (SAS) AF: 0.287 AC: 1382 AN: 4820

European-Finnish (FIN) AF: 0.288 AC: 3041 AN: 10552

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19376 AN: 67932

Other (OTH) AF: 0.401 AC: 846 AN: 2110

Alfa AF: 0.337 Hom.: 16387

Bravo AF: 0.430

Asia WGS AF: 0.365 AC: 1270 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.72
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1996720; hg19: chr8-113074096;