ENST00000836788.1:n.82-178A>G

Variant names:

• chr1-22648435-T-C
• rs294179
• ENST00000836788.1:n.82-178A>G

Variant summary

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

The ENST00000836788.1(ENSG00000308848):​n.82-178A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,058 control chromosomes in the GnomAD database, including 27,538 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 0.58 (27538 hom., cov: 32)
• Consequence: ENSG00000308848 ENST00000836788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 12 publications found

Genes affected

ENSG00000308848 (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 (AFR) allele frequency at 95% confidence interval = 0.828 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
ENSG00000308848	ENST00000836788.1	n.82-178A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87820 AN: 151938 Hom.: 27490 Cov.: 32

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.578 AC: 87919 AN: 152058 Hom.: 27538 Cov.: 32 AF XY: 0.577 AC XY: 42917 AN XY: 74354

African (AFR) AF: 0.835 AC: 34654 AN: 41488

American (AMR) AF: 0.528 AC: 8067 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1587 AN: 3472

East Asian (EAS) AF: 0.651 AC: 3358 AN: 5162

South Asian (SAS) AF: 0.608 AC: 2929 AN: 4818

European-Finnish (FIN) AF: 0.422 AC: 4469 AN: 10578

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31132 AN: 67944

Other (OTH) AF: 0.568 AC: 1201 AN: 2114

Alfa AF: 0.514 Hom.: 55736

Bravo AF: 0.597

Asia WGS AF: 0.662 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.7
DANN	Benign	0.47
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs294179; hg19: chr1-22974928;