2-78967292-A-G

Variant names:

• chr2-78967292-A-G
• rs1261238
• ENST00000776871.1:n.103+26765T>C

Variant summary

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

The ENST00000776871.1(ENSG00000286260):​n.103+26765T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 152,098 control chromosomes in the GnomAD database, including 51,555 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 0.82 (51555 hom., cov: 31)
• Consequence: ENSG00000286260 ENST00000776871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 2 publications found

Genes affected

ENSG00000286260 (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 (AFR) allele frequency at 95% confidence interval = 0.944 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776871.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286260	ENST00000776871.1		n.103+26765T>C		intron	N/A
	ENSG00000286260	ENST00000776872.1		n.62+26765T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124386 AN: 151980 Hom.: 51496 Cov.: 31

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.756

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.819 AC: 124509 AN: 152098 Hom.: 51555 Cov.: 31 AF XY: 0.820 AC XY: 60976 AN XY: 74318

African (AFR) AF: 0.951 AC: 39516 AN: 41532

American (AMR) AF: 0.793 AC: 12112 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.756 AC: 2626 AN: 3472

East Asian (EAS) AF: 0.889 AC: 4581 AN: 5152

South Asian (SAS) AF: 0.763 AC: 3678 AN: 4818

European-Finnish (FIN) AF: 0.790 AC: 8325 AN: 10544

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51141 AN: 67986

Other (OTH) AF: 0.790 AC: 1665 AN: 2108

Alfa AF: 0.768 Hom.: 84348

Bravo AF: 0.823

Asia WGS AF: 0.851 AC: 2958 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.1
DANN	Benign	0.42
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1261238; hg19: chr2-79194418;