chr2-78939317-T-C

Variant names:

• chr2-78939317-T-C
• rs1261226
• ENST00000776871.1:n.104-24373A>G

Variant summary

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

The ENST00000776871.1(ENSG00000286260):​n.104-24373A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 151,876 control chromosomes in the GnomAD database, including 19,929 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 0.51 (19929 hom., cov: 32)
• Consequence: ENSG00000286260 ENST00000776871.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 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
ENSG00000286260	ENST00000776871.1	n.104-24373A>G		intron_variant	Intron 1 of 3
ENSG00000286260	ENST00000776872.1	n.63-24373A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.509 AC: 77266 AN: 151760 Hom.: 19913 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.580

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.509 AC: 77329 AN: 151876 Hom.: 19929 Cov.: 32 AF XY: 0.508 AC XY: 37716 AN XY: 74228

African (AFR) AF: 0.491 AC: 20306 AN: 41390

American (AMR) AF: 0.508 AC: 7752 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.580 AC: 2010 AN: 3468

East Asian (EAS) AF: 0.274 AC: 1415 AN: 5160

South Asian (SAS) AF: 0.429 AC: 2066 AN: 4816

European-Finnish (FIN) AF: 0.543 AC: 5716 AN: 10532

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36379 AN: 67926

Other (OTH) AF: 0.504 AC: 1066 AN: 2114

Alfa AF: 0.524 Hom.: 10510

Bravo AF: 0.507

Asia WGS AF: 0.347 AC: 1204 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.11
DANN	Benign	0.41
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs1261226; hg19: chr2-79166443;