2-112799290-C-T

Variant names:

• chr2-112799290-C-T
• rs11898680
• ENST00000762706.1:n.404+28394C>T

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+28394C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 113,902 control chromosomes in the GnomAD database, including 5,676 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 0.35 (5676 hom., cov: 21)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284
• Publications: 8 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.398 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
ENSG00000299339	ENST00000762706.1	n.404+28394C>T		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.499+28394C>T		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.265+28394C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.350 AC: 39793 AN: 113836 Hom.: 5674 Cov.: 21

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.477

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.350 AC: 39814 AN: 113902 Hom.: 5676 Cov.: 21 AF XY: 0.358 AC XY: 19415 AN XY: 54284

African (AFR) AF: 0.265 AC: 7379 AN: 27872

American (AMR) AF: 0.409 AC: 4160 AN: 10182

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1208 AN: 3068

East Asian (EAS) AF: 0.137 AC: 448 AN: 3278

South Asian (SAS) AF: 0.366 AC: 1262 AN: 3450

European-Finnish (FIN) AF: 0.492 AC: 3204 AN: 6510

Middle Eastern (MID) AF: 0.475 AC: 115 AN: 242

European-Non Finnish (NFE) AF: 0.371 AC: 21106 AN: 56938

Other (OTH) AF: 0.368 AC: 565 AN: 1534

Alfa AF: 0.210 Hom.: 619

Bravo AF: 0.260

Asia WGS AF: 0.201 AC: 703 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.8
DANN	Benign	0.58
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11898680; hg19: chr2-113556867;