chr3-182733495-C-G

Variant names:

• chr3-182733495-C-G
• rs2700848
• ENST00000788512.1:n.206+29790C>G

Variant summary

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

The ENST00000788512.1(ENSG00000302649):​n.206+29790C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 151,914 control chromosomes in the GnomAD database, including 13,217 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 0.40 (13217 hom., cov: 32)
• Consequence: ENSG00000302649 ENST00000788512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 3 publications found

Genes affected

ENSG00000302649 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788512.1. 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
	ENSG00000302649	ENST00000788512.1		n.206+29790C>G		intron	N/A
	ENSG00000302649	ENST00000788513.1		n.201+29790C>G		intron	N/A
	ENSG00000302649	ENST00000788514.1		n.201+29790C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61407 AN: 151794 Hom.: 13181 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.405 AC: 61506 AN: 151914 Hom.: 13217 Cov.: 32 AF XY: 0.402 AC XY: 29847 AN XY: 74254

African (AFR) AF: 0.544 AC: 22511 AN: 41372

American (AMR) AF: 0.397 AC: 6056 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1933 AN: 3468

East Asian (EAS) AF: 0.437 AC: 2257 AN: 5162

South Asian (SAS) AF: 0.375 AC: 1804 AN: 4814

European-Finnish (FIN) AF: 0.289 AC: 3054 AN: 10570

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.332 AC: 22561 AN: 67962

Other (OTH) AF: 0.426 AC: 900 AN: 2112

Alfa AF: 0.219 Hom.: 466

Bravo AF: 0.419

Asia WGS AF: 0.442 AC: 1534 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.36
DANN	Benign	0.35
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2700848; hg19: chr3-182451283;