ENST00000762776.1:n.208-17785C>A

Variant names:

• chr2-156743649-G-T
• rs2882945
• ENST00000762776.1:n.208-17785C>A

Variant summary

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

The ENST00000762776.1(ENSG00000299347):​n.208-17785C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.46 in 151,894 control chromosomes in the GnomAD database, including 16,651 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 0.46 (16651 hom., cov: 32)
• Consequence: ENSG00000299347 ENST00000762776.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.998
• Publications: 1 publications found

Genes affected

ENSG00000299347 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.52 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
ENSG00000299347	ENST00000762776.1	n.208-17785C>A		intron_variant	Intron 1 of 1
ENSG00000299347	ENST00000762777.1	n.328-17785C>A		intron_variant	Intron 2 of 2
ENSG00000299347	ENST00000762778.1	n.239-17785C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69924 AN: 151776 Hom.: 16641 Cov.: 32

Gnomad AFR AF: 0.421

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.460 AC: 69946 AN: 151894 Hom.: 16651 Cov.: 32 AF XY: 0.454 AC XY: 33694 AN XY: 74242

African (AFR) AF: 0.421 AC: 17425 AN: 41412

American (AMR) AF: 0.338 AC: 5154 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1483 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1480 AN: 5154

South Asian (SAS) AF: 0.484 AC: 2320 AN: 4798

European-Finnish (FIN) AF: 0.467 AC: 4924 AN: 10544

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.525 AC: 35651 AN: 67936

Other (OTH) AF: 0.451 AC: 954 AN: 2114

Alfa AF: 0.383 Hom.: 1092

Bravo AF: 0.442

Asia WGS AF: 0.395 AC: 1371 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.052
DANN	Benign	0.43
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2882945; hg19: chr2-157600161;