2-78036757-T-C

Variant names:

• chr2-78036757-T-C
• rs1527194
• ENST00000667782.1:n.83-96871A>G

Variant summary

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

The ENST00000667782.1(ENSG00000227088):​n.83-96871A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.867 in 152,098 control chromosomes in the GnomAD database, including 57,491 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 0.87 (57491 hom., cov: 31)
• Consequence: ENSG00000227088 ENST00000667782.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 0 publications found

Genes affected

ENSG00000227088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927967	NR_110288.1	n.345-161695A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227088	ENST00000667782.1	n.83-96871A>G		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.867 AC: 131817 AN: 151980 Hom.: 57436 Cov.: 31

Gnomad AFR AF: 0.950

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.829

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.868

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.818

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.867 AC: 131931 AN: 152098 Hom.: 57491 Cov.: 31 AF XY: 0.871 AC XY: 64751 AN XY: 74342

African (AFR) AF: 0.950 AC: 39450 AN: 41524

American (AMR) AF: 0.850 AC: 12984 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.829 AC: 2876 AN: 3470

East Asian (EAS) AF: 0.903 AC: 4647 AN: 5146

South Asian (SAS) AF: 0.908 AC: 4375 AN: 4816

European-Finnish (FIN) AF: 0.868 AC: 9181 AN: 10582

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.818 AC: 55571 AN: 67972

Other (OTH) AF: 0.870 AC: 1839 AN: 2114

Alfa AF: 0.832 Hom.: 26752

Bravo AF: 0.869

Asia WGS AF: 0.922 AC: 3206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.65
DANN	Benign	0.66
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1527194; hg19: chr2-78263883;