rs2804923

Variant names:

• chr6-13573631-C-T
• rs2804923
• ENST00000769395.1:n.199+334G>A

Variant summary

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

The ENST00000769395.1(ENSG00000300133):​n.199+334G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,944 control chromosomes in the GnomAD database, including 26,429 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 0.59 (26429 hom., cov: 31)
• Consequence: ENSG00000300133 ENST00000769395.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.161
• Publications: 2 publications found

Genes affected

ENSG00000300133 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374937	XR_926497.4	n.470+334G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300133	ENST00000769395.1	n.199+334G>A		intron_variant	Intron 1 of 1
ENSG00000300133	ENST00000769396.1	n.199+334G>A		intron_variant	Intron 1 of 1
ENSG00000300152	ENST00000769526.1	n.-203C>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88933 AN: 151826 Hom.: 26375 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.586 AC: 89047 AN: 151944 Hom.: 26429 Cov.: 31 AF XY: 0.586 AC XY: 43498 AN XY: 74244

African (AFR) AF: 0.542 AC: 22428 AN: 41392

American (AMR) AF: 0.675 AC: 10320 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.518 AC: 1796 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1720 AN: 5148

South Asian (SAS) AF: 0.616 AC: 2964 AN: 4812

European-Finnish (FIN) AF: 0.606 AC: 6398 AN: 10558

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41273 AN: 67970

Other (OTH) AF: 0.610 AC: 1284 AN: 2106

Alfa AF: 0.577 Hom.: 4275

Bravo AF: 0.584

Asia WGS AF: 0.522 AC: 1816 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.35
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2804923; hg19: chr6-13573863;