chr2-221354591-C-T

Variant names:

• chr2-221354591-C-T
• rs1346799
• ENST00000702411.2:n.375+17981G>A

Variant summary

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

The ENST00000702411.2(ENSG00000290000):​n.375+17981G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 151,108 control chromosomes in the GnomAD database, including 11,412 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 0.37 (11412 hom., cov: 30)
• Consequence: ENSG00000290000 ENST00000702411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 0 publications found

Genes affected

ENSG00000290000 (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 (AFR) allele frequency at 95% confidence interval = 0.553 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
ENSG00000290000	ENST00000702411.2	n.375+17981G>A		intron_variant	Intron 1 of 2
ENSG00000290000	ENST00000798102.1	n.146-3223G>A		intron_variant	Intron 1 of 3
ENSG00000290000	ENST00000798103.1	n.89+17981G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.370 AC: 55838 AN: 150992 Hom.: 11394 Cov.: 30

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.370 AC: 55904 AN: 151108 Hom.: 11412 Cov.: 30 AF XY: 0.366 AC XY: 26993 AN XY: 73762

African (AFR) AF: 0.559 AC: 23001 AN: 41146

American (AMR) AF: 0.337 AC: 5099 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 681 AN: 3462

East Asian (EAS) AF: 0.204 AC: 1046 AN: 5136

South Asian (SAS) AF: 0.208 AC: 992 AN: 4774

European-Finnish (FIN) AF: 0.310 AC: 3236 AN: 10440

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.307 AC: 20808 AN: 67750

Other (OTH) AF: 0.318 AC: 662 AN: 2084

Alfa AF: 0.315 Hom.: 4032

Bravo AF: 0.383

Asia WGS AF: 0.229 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.78
DANN	Benign	0.63
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1346799; hg19: chr2-222219311;