2-201994894-G-A

Variant names:

• chr2-201994894-G-A
• rs6754521
• ENST00000608741.2:n.976-23818C>T

Variant summary

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

The ENST00000608741.2(ENSG00000273209):​n.976-23818C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 151,074 control chromosomes in the GnomAD database, including 5,463 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 0.25 (5463 hom., cov: 30)
• Consequence: ENSG00000273209 ENST00000608741.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 2 publications found

Genes affected

ENSG00000273209 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 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
ENSG00000273209	ENST00000608741.2	n.976-23818C>T		intron_variant	Intron 1 of 1	6
ENSG00000289026	ENST00000738740.1	n.142+23816G>A		intron_variant	Intron 1 of 1
ENSG00000289026	ENST00000738741.1	n.321+22146G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37715 AN: 150990 Hom.: 5463 Cov.: 30

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0810

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.250 AC: 37715 AN: 151074 Hom.: 5463 Cov.: 30 AF XY: 0.242 AC XY: 17859 AN XY: 73750

African (AFR) AF: 0.134 AC: 5530 AN: 41184

American (AMR) AF: 0.229 AC: 3480 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3470

East Asian (EAS) AF: 0.0807 AC: 416 AN: 5158

South Asian (SAS) AF: 0.342 AC: 1637 AN: 4784

European-Finnish (FIN) AF: 0.194 AC: 1980 AN: 10180

Middle Eastern (MID) AF: 0.375 AC: 108 AN: 288

European-Non Finnish (NFE) AF: 0.335 AC: 22709 AN: 67826

Other (OTH) AF: 0.275 AC: 575 AN: 2092

Alfa AF: 0.296 Hom.: 3209

Bravo AF: 0.245

Asia WGS AF: 0.224 AC: 780 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.9
DANN	Benign	0.79
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs6754521; hg19: chr2-202859617;