8-76236495-A-T

Variant names:

• chr8-76236495-A-T
• rs12680321
• ENST00000668249.2:n.310+69843T>A

Variant summary

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

The ENST00000668249.2(ENSG00000287352):​n.310+69843T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,076 control chromosomes in the GnomAD database, including 2,661 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 0.17 (2661 hom., cov: 32)
• Consequence: ENSG00000287352 ENST00000668249.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 1 publications found

Genes affected

ENSG00000287352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724858	XR_001745961.3	n.286+69843T>A		intron_variant	Intron 2 of 4
LOC102724858	XR_007060967.1	n.298+69843T>A		intron_variant	Intron 2 of 2
LOC102724858	XR_007060968.1	n.281+69843T>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287352	ENST00000668249.2	n.310+69843T>A		intron_variant	Intron 2 of 2
ENSG00000287352	ENST00000824976.1	n.251+69843T>A		intron_variant	Intron 2 of 4
ENSG00000287352	ENST00000824977.1	n.259+69843T>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25652 AN: 151958 Hom.: 2664 Cov.: 32

Gnomad AFR AF: 0.0451

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.228

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.169 AC: 25636 AN: 152076 Hom.: 2661 Cov.: 32 AF XY: 0.168 AC XY: 12460 AN XY: 74348

African (AFR) AF: 0.0450 AC: 1868 AN: 41542

American (AMR) AF: 0.209 AC: 3185 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 747 AN: 3468

East Asian (EAS) AF: 0.125 AC: 647 AN: 5180

South Asian (SAS) AF: 0.155 AC: 744 AN: 4814

European-Finnish (FIN) AF: 0.213 AC: 2248 AN: 10558

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.228 AC: 15496 AN: 67952

Other (OTH) AF: 0.185 AC: 389 AN: 2108

Alfa AF: 0.188 Hom.: 373

Bravo AF: 0.165

Asia WGS AF: 0.117 AC: 409 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
DANN	Benign	0.50
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs12680321; hg19: chr8-77148730;