chr9-21701433-T-C

Variant names:

• chr9-21701433-T-C
• rs7848524
• ENST00000765951.1:n.107-9169T>C

Variant summary

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

The ENST00000765951.1(ENSG00000299739):​n.107-9169T>C 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 151,692 control chromosomes in the GnomAD database, including 28,410 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 (28410 hom., cov: 31)
• Consequence: ENSG00000299739 ENST00000765951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 11 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 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.107-9169T>C		intron	N/A
	ENSG00000299763	ENST00000766147.1		n.452+1484A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91070 AN: 151574 Hom.: 28399 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.687

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.601 AC: 91125 AN: 151692 Hom.: 28410 Cov.: 31 AF XY: 0.596 AC XY: 44195 AN XY: 74114

African (AFR) AF: 0.781 AC: 32309 AN: 41368

American (AMR) AF: 0.500 AC: 7623 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2001 AN: 3464

East Asian (EAS) AF: 0.687 AC: 3553 AN: 5172

South Asian (SAS) AF: 0.429 AC: 2058 AN: 4798

European-Finnish (FIN) AF: 0.542 AC: 5690 AN: 10498

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.533 AC: 36133 AN: 67818

Other (OTH) AF: 0.582 AC: 1229 AN: 2112

Alfa AF: 0.533 Hom.: 36405

Bravo AF: 0.609

Asia WGS AF: 0.526 AC: 1830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.19
DANN	Benign	0.43
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7848524; hg19: chr9-21701432;