9-21707373-C-T

Variant names:

• chr9-21707373-C-T
• rs751173
• ENST00000765951.1:n.107-3229C>T

Variant summary

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

The ENST00000765951.1(ENSG00000299739):​n.107-3229C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.601 in 151,510 control chromosomes in the GnomAD database, including 28,324 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 0.60 (28324 hom., cov: 30)
• Consequence: ENSG00000299739 ENST00000765951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 10 publications found

Genes affected

ENSG00000299739 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765951.1. 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
	ENSG00000299739	ENST00000765951.1		n.107-3229C>T		intron	N/A
	ENSG00000299763	ENST00000766147.1		n.231+1597G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91050 AN: 151412 Hom.: 28312 Cov.: 30

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.690

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.601 AC: 91101 AN: 151510 Hom.: 28324 Cov.: 30 AF XY: 0.597 AC XY: 44159 AN XY: 73996

African (AFR) AF: 0.769 AC: 31739 AN: 41290

American (AMR) AF: 0.501 AC: 7612 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2013 AN: 3466

East Asian (EAS) AF: 0.690 AC: 3560 AN: 5160

South Asian (SAS) AF: 0.434 AC: 2076 AN: 4788

European-Finnish (FIN) AF: 0.547 AC: 5682 AN: 10392

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36647 AN: 67908

Other (OTH) AF: 0.588 AC: 1240 AN: 2110

Alfa AF: 0.542 Hom.: 15253

Bravo AF: 0.609

Asia WGS AF: 0.528 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	15
DANN	Benign	0.68
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs751173; hg19: chr9-21707372;