ENST00000805798.1:n.296-62C>T

Variant names:

• chr2-18552806-C-T
• rs16985278
• ENST00000805798.1:n.296-62C>T

Variant summary

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

The ENST00000805798.1(ENSG00000304724):​n.296-62C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.343 in 152,018 control chromosomes in the GnomAD database, including 10,953 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 0.34 (10953 hom., cov: 32)
• Consequence: ENSG00000304724 ENST00000805798.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 3 publications found

Genes affected

ENSG00000304724 (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 (AFR) allele frequency at 95% confidence interval = 0.589 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
ENSG00000304724	ENST00000805798.1	n.296-62C>T		intron_variant	Intron 3 of 4
ENSG00000304724	ENST00000805799.1	n.239-62C>T		intron_variant	Intron 4 of 5
ENSG00000304724	ENST00000805800.1	n.224-62C>T		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.343 AC: 52067 AN: 151900 Hom.: 10922 Cov.: 32

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.0465

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.343 AC: 52148 AN: 152018 Hom.: 10953 Cov.: 32 AF XY: 0.336 AC XY: 24987 AN XY: 74320

African (AFR) AF: 0.595 AC: 24641 AN: 41414

American (AMR) AF: 0.291 AC: 4446 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3466

East Asian (EAS) AF: 0.0468 AC: 242 AN: 5176

South Asian (SAS) AF: 0.185 AC: 893 AN: 4820

European-Finnish (FIN) AF: 0.253 AC: 2672 AN: 10574

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17567 AN: 67970

Other (OTH) AF: 0.309 AC: 651 AN: 2110

Alfa AF: 0.278 Hom.: 10931

Bravo AF: 0.355

Asia WGS AF: 0.156 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.85
DANN	Benign	0.21
PhyloP100		0.032

Splicing

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

Other links and lift over

dbSNP: rs16985278; hg19: chr2-18734072;