rs512089

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-23874049-A-C
• chr9-23874049-A-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375993	XR_929520.3	n.459+20723A>C		intron_variant	Intron 2 of 4
LOC105375993	XR_929521.3	n.459+20723A>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300787	ENST00000774067.1	n.406+20723A>C		intron_variant	Intron 2 of 2
ENSG00000300787	ENST00000774068.1	n.441-16800A>C		intron_variant	Intron 2 of 3
ENSG00000300787	ENST00000774069.1	n.395-16857A>C		intron_variant	Intron 2 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs512089; hg19: chr9-23874047;