2-112814780-T-C

Variant names:

• chr2-112814780-T-C
• rs12469600
• ENST00000762706.1:n.404+43884T>C

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+43884T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 152,170 control chromosomes in the GnomAD database, including 3,980 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 0.22 (3980 hom., cov: 31)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 12 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.257 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+43884T>C		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.499+43884T>C		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.265+43884T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33530 AN: 152052 Hom.: 3981 Cov.: 31

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.294

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.220 AC: 33532 AN: 152170 Hom.: 3980 Cov.: 31 AF XY: 0.223 AC XY: 16593 AN XY: 74396

African (AFR) AF: 0.136 AC: 5668 AN: 41536

American (AMR) AF: 0.254 AC: 3887 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.294 AC: 1019 AN: 3470

East Asian (EAS) AF: 0.0923 AC: 478 AN: 5178

South Asian (SAS) AF: 0.269 AC: 1298 AN: 4818

European-Finnish (FIN) AF: 0.275 AC: 2914 AN: 10584

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17348 AN: 67974

Other (OTH) AF: 0.238 AC: 503 AN: 2116

Alfa AF: 0.239 Hom.: 8379

Bravo AF: 0.212

Asia WGS AF: 0.190 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.76
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs12469600; hg19: chr2-113572357;