13-45943924-C-T

Variant names:

• chr13-45943924-C-T
• rs2806922
• ENST00000766969.1:n.1285C>T

Variant summary

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

The ENST00000766969.1(ENSG00000299862):​n.1285C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,122 control chromosomes in the GnomAD database, including 5,723 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 (5723 hom., cov: 33)
• Consequence: ENSG00000299862 ENST00000766969.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 3 publications found

Genes affected

ENSG00000299862 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766969.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299862	ENST00000766969.1		n.1285C>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40804 AN: 152004 Hom.: 5714 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.268 AC: 40835 AN: 152122 Hom.: 5723 Cov.: 33 AF XY: 0.263 AC XY: 19572 AN XY: 74370

African (AFR) AF: 0.211 AC: 8766 AN: 41492

American (AMR) AF: 0.272 AC: 4149 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1209 AN: 3468

East Asian (EAS) AF: 0.196 AC: 1017 AN: 5180

South Asian (SAS) AF: 0.289 AC: 1393 AN: 4818

European-Finnish (FIN) AF: 0.218 AC: 2301 AN: 10554

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20866 AN: 68012

Other (OTH) AF: 0.317 AC: 670 AN: 2116

Alfa AF: 0.273 Hom.: 1014

Bravo AF: 0.271

Asia WGS AF: 0.240 AC: 833 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.46
PhyloP100		-0.033

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2806922;

hg19: chr13-46518059;

COSMIC: COSV69348967;