ENST00000764873.1:n.413+6124T>C

Variant names:

• chr9-101748176-T-C
• rs10512289
• ENST00000764873.1:n.413+6124T>C

Variant summary

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

The ENST00000764873.1(ENSG00000299588):​n.413+6124T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0706 in 152,040 control chromosomes in the GnomAD database, including 804 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 0.071 (804 hom., cov: 32)
• Consequence: ENSG00000299588 ENST00000764873.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 2 publications found

Genes affected

ENSG00000299588 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000764873.1. 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
	ENSG00000299588	ENST00000764873.1		n.413+6124T>C		intron	N/A
	ENSG00000299588	ENST00000764874.1		n.247+6124T>C		intron	N/A
	ENSG00000299588	ENST00000764876.1		n.248+6124T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10716 AN: 151922 Hom.: 802 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0400

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.0294

Gnomad FIN AF: 0.0278

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0210

Gnomad OTH AF: 0.0595

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

GnomAD4 genome AF: 0.0706 AC: 10739 AN: 152040 Hom.: 804 Cov.: 32 AF XY: 0.0700 AC XY: 5202 AN XY: 74346

African (AFR) AF: 0.192 AC: 7978 AN: 41490

American (AMR) AF: 0.0399 AC: 608 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3460

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5168

South Asian (SAS) AF: 0.0298 AC: 144 AN: 4832

European-Finnish (FIN) AF: 0.0278 AC: 295 AN: 10610

Middle Eastern (MID) AF: 0.0719 AC: 21 AN: 292

European-Non Finnish (NFE) AF: 0.0210 AC: 1424 AN: 67924

Other (OTH) AF: 0.0641 AC: 135 AN: 2106

Alfa AF: 0.0847 Hom.: 493

Bravo AF: 0.0759

Asia WGS AF: 0.0400 AC: 140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.78
DANN	Benign	0.47
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs10512289; hg19: chr9-104510458;