ENST00000774883.1:n.295-30192A>G

Variant names:

• chr12-115064913-A-G
• rs2194980
• ENST00000774883.1:n.295-30192A>G

Variant summary

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

The ENST00000774883.1(ENSG00000300895):​n.295-30192A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 151,966 control chromosomes in the GnomAD database, including 35,101 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 0.67 (35101 hom., cov: 31)
• Consequence: ENSG00000300895 ENST00000774883.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 14 publications found

Genes affected

ENSG00000300895 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723639	XR_001749334.2	n.441-12311A>G		intron_variant	Intron 2 of 2
LOC102723639	XR_007063588.1	n.1505+2056A>G		intron_variant	Intron 4 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300895	ENST00000774883.1	n.295-30192A>G		intron_variant	Intron 2 of 3
ENSG00000300895	ENST00000774884.1	n.321-12311A>G		intron_variant	Intron 3 of 3
ENSG00000300895	ENST00000774885.1	n.546+2056A>G		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.672 AC: 101970 AN: 151848 Hom.: 35074 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.672 AC: 102046 AN: 151966 Hom.: 35101 Cov.: 31 AF XY: 0.671 AC XY: 49813 AN XY: 74274

African (AFR) AF: 0.799 AC: 33154 AN: 41470

American (AMR) AF: 0.535 AC: 8160 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.719 AC: 2494 AN: 3470

East Asian (EAS) AF: 0.379 AC: 1959 AN: 5164

South Asian (SAS) AF: 0.618 AC: 2960 AN: 4792

European-Finnish (FIN) AF: 0.725 AC: 7658 AN: 10560

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43396 AN: 67944

Other (OTH) AF: 0.650 AC: 1371 AN: 2108

Alfa AF: 0.641 Hom.: 131709

Bravo AF: 0.658

Asia WGS AF: 0.505 AC: 1756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.074
DANN	Benign	0.47
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs2194980; hg19: chr12-115502718;