rs2796304

Variant names:

• chr10-29277054-C-A
• rs2796304
• ENST00000808501.1:n.*247G>T

Variant summary

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

The ENST00000808501.1(ENSG00000305098):​n.*247G>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,986 control chromosomes in the GnomAD database, including 20,352 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 0.52 (20352 hom., cov: 33)
• Consequence: ENSG00000305098 ENST00000808501.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675
• Publications: 1 publications found

Genes affected

ENSG00000305098 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808501.1. 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
	ENSG00000305098	ENST00000808501.1		n.*247G>T		downstream_gene	N/A
	ENSG00000305098	ENST00000808502.1		n.*243G>T		downstream_gene	N/A
	ENSG00000305098	ENST00000808503.1		n.*243G>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78463 AN: 151866 Hom.: 20330 Cov.: 33

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.620

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.509

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.517 AC: 78503 AN: 151986 Hom.: 20352 Cov.: 33 AF XY: 0.515 AC XY: 38229 AN XY: 74280

African (AFR) AF: 0.492 AC: 20384 AN: 41442

American (AMR) AF: 0.466 AC: 7119 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.620 AC: 2151 AN: 3470

East Asian (EAS) AF: 0.398 AC: 2056 AN: 5164

South Asian (SAS) AF: 0.509 AC: 2452 AN: 4816

European-Finnish (FIN) AF: 0.490 AC: 5168 AN: 10546

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37534 AN: 67956

Other (OTH) AF: 0.515 AC: 1087 AN: 2112

Alfa AF: 0.527 Hom.: 10518

Bravo AF: 0.508

Asia WGS AF: 0.432 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.15
DANN	Benign	0.59
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs2796304; hg19: chr10-29565983;