chr8-72451754-T-G

Variant names:

• chr8-72451754-T-G
• rs2116078
• ENST00000830790.1:n.209-1409A>C

Variant summary

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

The ENST00000830790.1(ENSG00000308060):​n.209-1409A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,994 control chromosomes in the GnomAD database, including 15,634 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 0.43 (15634 hom., cov: 32)
• Consequence: ENSG00000308060 ENST00000830790.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202
• Publications: 9 publications found

Genes affected

ENSG00000308060 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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
ENSG00000308060	ENST00000830790.1	n.209-1409A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.431 AC: 65504 AN: 151874 Hom.: 15619 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.594

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.431 AC: 65554 AN: 151994 Hom.: 15634 Cov.: 32 AF XY: 0.431 AC XY: 32045 AN XY: 74288

African (AFR) AF: 0.227 AC: 9407 AN: 41464

American (AMR) AF: 0.488 AC: 7457 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.563 AC: 1955 AN: 3470

East Asian (EAS) AF: 0.292 AC: 1506 AN: 5150

South Asian (SAS) AF: 0.315 AC: 1518 AN: 4816

European-Finnish (FIN) AF: 0.536 AC: 5661 AN: 10560

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36431 AN: 67954

Other (OTH) AF: 0.450 AC: 949 AN: 2110

Alfa AF: 0.490 Hom.: 39931

Bravo AF: 0.420

Asia WGS AF: 0.358 AC: 1242 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.64
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2116078; hg19: chr8-73363989;