2-21077898-C-A

Variant names:

• chr2-21077898-C-A
• rs1429974
• ENST00000821616.1:n.239+18456G>T

Variant summary

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

The ENST00000821616.1(ENSG00000287956):​n.239+18456G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,964 control chromosomes in the GnomAD database, including 6,498 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 0.29 (6498 hom., cov: 32)
• Consequence: ENSG00000287956 ENST00000821616.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 17 publications found

Genes affected

ENSG00000287956 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124905593	XR_007088659.1	n.578+6767C>A		intron_variant	Intron 1 of 2
LOC124905593	XR_007088660.1	n.578+6767C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287956	ENST00000821616.1	n.239+18456G>T		intron_variant	Intron 1 of 1
ENSG00000287956	ENST00000821617.1	n.261+18456G>T		intron_variant	Intron 1 of 2
ENSG00000287956	ENST00000821618.1	n.242-10257G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44096 AN: 151844 Hom.: 6496 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.290 AC: 44124 AN: 151964 Hom.: 6498 Cov.: 32 AF XY: 0.287 AC XY: 21350 AN XY: 74268

African (AFR) AF: 0.258 AC: 10706 AN: 41446

American (AMR) AF: 0.325 AC: 4949 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 870 AN: 3466

East Asian (EAS) AF: 0.268 AC: 1385 AN: 5168

South Asian (SAS) AF: 0.177 AC: 849 AN: 4808

European-Finnish (FIN) AF: 0.272 AC: 2867 AN: 10544

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21546 AN: 67972

Other (OTH) AF: 0.270 AC: 570 AN: 2110

Alfa AF: 0.284 Hom.: 5697

Bravo AF: 0.297

Asia WGS AF: 0.218 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.2
DANN	Benign	0.55
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1429974; hg19: chr2-21300770;