chr2-16276762-A-G

Variant names:

• chr2-16276762-A-G
• rs340764
• ENST00000420404.2:n.965+47496A>G

Variant summary

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

The ENST00000420404.2(ENSG00000228876):​n.965+47496A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 151,978 control chromosomes in the GnomAD database, including 24,758 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 0.56 (24758 hom., cov: 32)
• Consequence: ENSG00000228876 ENST00000420404.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 1 publications found

Genes affected

ENSG00000228876 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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
ENSG00000228876	ENST00000420404.2	n.965+47496A>G		intron_variant	Intron 3 of 3	3
ENSG00000228876	ENST00000642208.1	n.294-22079A>G		intron_variant	Intron 2 of 2
ENSG00000228876	ENST00000644340.1	n.286-1765A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84290 AN: 151860 Hom.: 24710 Cov.: 32

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.827

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.555 AC: 84397 AN: 151978 Hom.: 24758 Cov.: 32 AF XY: 0.562 AC XY: 41701 AN XY: 74252

African (AFR) AF: 0.706 AC: 29269 AN: 41470

American (AMR) AF: 0.550 AC: 8401 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1706 AN: 3464

East Asian (EAS) AF: 0.827 AC: 4260 AN: 5152

South Asian (SAS) AF: 0.742 AC: 3572 AN: 4814

European-Finnish (FIN) AF: 0.488 AC: 5131 AN: 10520

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30486 AN: 67960

Other (OTH) AF: 0.511 AC: 1081 AN: 2114

Alfa AF: 0.420 Hom.: 1612

Bravo AF: 0.560

Asia WGS AF: 0.786 AC: 2731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.44
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs340764; hg19: chr2-16458030;