rs263640

Variant names:

• chr9-17019123-G-A
• rs263640
• ENST00000430545.4:n.270+334G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-17019123-G-A
• chr9-17019123-G-C

Variant summary

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

The ENST00000649137.2(ENSG00000237153):​n.1591-29796G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,054 control chromosomes in the GnomAD database, including 8,948 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 0.24 (8948 hom., cov: 32)
• Consequence: ENSG00000237153 ENST00000649137.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 6 publications found

Genes affected

ENSG00000237153 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649137.2. 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
	ENSG00000237153	ENST00000430545.4	TSL:5	n.270+334G>A		intron	N/A
	ENSG00000237153	ENST00000649137.2		n.1591-29796G>A		intron	N/A
	ENSG00000237153	ENST00000824948.1		n.98+503G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36694 AN: 151936 Hom.: 8914 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.0534

Gnomad EAS AF: 0.0910

Gnomad SAS AF: 0.0839

Gnomad FIN AF: 0.0630

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0963

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.242 AC: 36778 AN: 152054 Hom.: 8948 Cov.: 32 AF XY: 0.232 AC XY: 17264 AN XY: 74336

African (AFR) AF: 0.629 AC: 26062 AN: 41424

American (AMR) AF: 0.129 AC: 1962 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0534 AC: 185 AN: 3466

East Asian (EAS) AF: 0.0911 AC: 470 AN: 5162

South Asian (SAS) AF: 0.0844 AC: 407 AN: 4824

European-Finnish (FIN) AF: 0.0630 AC: 668 AN: 10604

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0963 AC: 6549 AN: 67990

Other (OTH) AF: 0.185 AC: 391 AN: 2112

Alfa AF: 0.121 Hom.: 3732

Bravo AF: 0.264

Asia WGS AF: 0.114 AC: 400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.33
DANN	Benign	0.53
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs263640; hg19: chr9-17019121;