chr9-23874049-A-C

Variant names:

• chr9-23874049-A-C
• rs512089
• ENST00000774067.1:n.406+20723A>C

Variant summary

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

The ENST00000774067.1(ENSG00000300787):​n.406+20723A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 151,708 control chromosomes in the GnomAD database, including 2,971 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 0.17 (2971 hom., cov: 32)
• Consequence: ENSG00000300787 ENST00000774067.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484
• Publications: 4 publications found

Genes affected

ENSG00000300787 (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 (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774067.1. 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
	ENSG00000300787	ENST00000774067.1		n.406+20723A>C		intron	N/A
	ENSG00000300787	ENST00000774068.1		n.441-16800A>C		intron	N/A
	ENSG00000300787	ENST00000774069.1		n.395-16857A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26277 AN: 151590 Hom.: 2973 Cov.: 32

Gnomad AFR AF: 0.0472

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.0410

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.173 AC: 26269 AN: 151708 Hom.: 2971 Cov.: 32 AF XY: 0.168 AC XY: 12452 AN XY: 74182

African (AFR) AF: 0.0471 AC: 1956 AN: 41518

American (AMR) AF: 0.142 AC: 2163 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 864 AN: 3450

East Asian (EAS) AF: 0.0411 AC: 213 AN: 5178

South Asian (SAS) AF: 0.165 AC: 794 AN: 4824

European-Finnish (FIN) AF: 0.201 AC: 2123 AN: 10580

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17519 AN: 67656

Other (OTH) AF: 0.158 AC: 332 AN: 2104

Alfa AF: 0.215 Hom.: 2082

Bravo AF: 0.163

Asia WGS AF: 0.0930 AC: 321 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.1
DANN	Benign	0.64
PhyloP100		0.48

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: rs512089;

hg19: chr9-23874047;