chr2-111496274-T-C

Variant names:

• chr2-111496274-T-C
• rs1345203
• ENST00000455309.2:n.391+4612T>C

Variant summary

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

The ENST00000455309.2(SOCAR):​n.391+4612T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 152,168 control chromosomes in the GnomAD database, including 6,101 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 0.27 (6101 hom., cov: 33)
• Consequence: SOCAR ENST00000455309.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120
• Publications: 9 publications found

Genes affected

SOCAR (HGNC:54421): (serous ovarian cancer associated RNA)

ENSG00000280878 (HGNC:):

MIR4435-2HG (HGNC:35163): (MIR4435-2 host gene)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000455309.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCAR	NR_187145.1		n.223+4612T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SOCAR	ENST00000455309.2	TSL:2	n.391+4612T>C		intron	N/A
	SOCAR	ENST00000627971.1	TSL:5	n.107+4612T>C		intron	N/A
	ENSG00000280878	ENST00000630717.1	TSL:5	n.26+27439T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40897 AN: 152050 Hom.: 6100 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.269 AC: 40908 AN: 152168 Hom.: 6101 Cov.: 33 AF XY: 0.269 AC XY: 20017 AN XY: 74400

African (AFR) AF: 0.380 AC: 15768 AN: 41480

American (AMR) AF: 0.243 AC: 3713 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 849 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2454 AN: 5174

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4822

European-Finnish (FIN) AF: 0.164 AC: 1742 AN: 10610

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14220 AN: 67994

Other (OTH) AF: 0.260 AC: 550 AN: 2116

Alfa AF: 0.176 Hom.: 709

Bravo AF: 0.281

Asia WGS AF: 0.402 AC: 1399 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.4
DANN	Benign	0.86
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs1345203; hg19: chr2-112253851;