8-36988591-C-T

Variant names:

• chr8-36988591-C-T
• rs7816345
• ENST00000817282.1:n.28-6805G>A

Variant summary

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

The ENST00000817282.1(ENSG00000306370):​n.28-6805G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,114 control chromosomes in the GnomAD database, including 5,944 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 0.26 (5944 hom., cov: 33)
• Consequence: ENSG00000306370 ENST00000817282.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.743
• Publications: 37 publications found

Genes affected

ENSG00000306370 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000306370	ENST00000817282.1	n.28-6805G>A		intron_variant	Intron 1 of 2
ENSG00000243503	ENST00000495560.2	n.-179G>A		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39377 AN: 151996 Hom.: 5941 Cov.: 33

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.259 AC: 39397 AN: 152114 Hom.: 5944 Cov.: 33 AF XY: 0.259 AC XY: 19268 AN XY: 74358

African (AFR) AF: 0.405 AC: 16813 AN: 41476

American (AMR) AF: 0.232 AC: 3550 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3470

East Asian (EAS) AF: 0.332 AC: 1711 AN: 5160

South Asian (SAS) AF: 0.306 AC: 1475 AN: 4826

European-Finnish (FIN) AF: 0.137 AC: 1446 AN: 10592

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12495 AN: 67984

Other (OTH) AF: 0.255 AC: 540 AN: 2114

Alfa AF: 0.211 Hom.: 11758

Bravo AF: 0.267

Asia WGS AF: 0.260 AC: 900 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.71
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs7816345; hg19: chr8-36846109;