rs4636294

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr9-21747804-A-G
• chr9-21747804-A-T

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987026	XR_001746563.3	n.163+20021T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299739	ENST00000765951.1	n.154+37155A>G		intron_variant	Intron 2 of 2

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 v4.3

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;