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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000769395.1. 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
	ENSG00000300133	ENST00000769395.1		n.199+334G>A		intron	N/A
	ENSG00000300133	ENST00000769396.1		n.199+334G>A		intron	N/A
	ENSG00000300152	ENST00000769526.1		n.-203C>T		upstream_gene	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs2804923;

hg19: chr6-13573863;