chr9-21747804-A-G

Variant names:

• chr9-21747804-A-G
• rs4636294
• ENST00000765951.1:n.154+37155A>G

Variant summary

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

The ENST00000765951.1(ENSG00000299739):​n.154+37155A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 151,812 control chromosomes in the GnomAD database, including 28,560 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 (28560 hom., cov: 31)
• Consequence: ENSG00000299739 ENST00000765951.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263
• Publications: 43 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.782 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299739	ENST00000765951.1		n.154+37155A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.600 AC: 90984 AN: 151694 Hom.: 28505 Cov.: 31

Gnomad AFR AF: 0.788

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.600 AC: 91107 AN: 151812 Hom.: 28560 Cov.: 31 AF XY: 0.595 AC XY: 44115 AN XY: 74204

African (AFR) AF: 0.789 AC: 32685 AN: 41436

American (AMR) AF: 0.595 AC: 9053 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1799 AN: 3464

East Asian (EAS) AF: 0.695 AC: 3579 AN: 5148

South Asian (SAS) AF: 0.366 AC: 1765 AN: 4826

European-Finnish (FIN) AF: 0.515 AC: 5433 AN: 10552

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35100 AN: 67870

Other (OTH) AF: 0.569 AC: 1199 AN: 2106

Alfa AF: 0.540 Hom.: 93170

Bravo AF: 0.623

Asia WGS AF: 0.536 AC: 1863 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.50
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs4636294; hg19: chr9-21747803;