rs649057

Variant names:

• chr9-99472041-C-A
• rs649057
• ENST00000652827.1:n.231-8969G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-99472041-C-A
• chr9-99472041-C-G
• chr9-99472041-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652827.1(ENSG00000237461):​n.231-8969G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0834 in 152,278 control chromosomes in the GnomAD database, including 760 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 0.083 (760 hom., cov: 32)
• Consequence: ENSG00000237461 ENST00000652827.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

ENSG00000237461 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237461	ENST00000652827.1	n.231-8969G>T		intron_variant	Intron 2 of 5
STX17-DT	ENST00000655615.1	n.269-8969G>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0830 AC: 12628 AN: 152160 Hom.: 739 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.0139

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0505

Gnomad OTH AF: 0.0933

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

GnomAD4 genome AF: 0.0834 AC: 12699 AN: 152278 Hom.: 760 Cov.: 32 AF XY: 0.0845 AC XY: 6290 AN XY: 74476

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.0897

Gnomad4 FIN AF: 0.0139

Gnomad4 NFE AF: 0.0505

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.0647 Hom.: 525

Bravo AF: 0.102

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.72
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs649057; hg19: chr9-102234323;