rs2592991

Positions:

• chr9-85385591-C-A
• chr9-85385591-C-G
• chr9-85385591-C-T

Variant summary

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

The ENST00000669133.1(ENSG00000285634):​n.283-12631G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 152,242 control chromosomes in the GnomAD database, including 58,385 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 0.87 (58385 hom., cov: 31)
• Consequence: ENST00000669133.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000669133.1	n.283-12631G>T		intron_variant, non_coding_transcript_variant
	ENST00000648131.1	n.601-12631G>T		intron_variant, non_coding_transcript_variant
	ENST00000662737.1	n.1681-12631G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132765 AN: 152124 Hom.: 58343 Cov.: 31

Gnomad AFR AF: 0.948

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.851

Gnomad OTH AF: 0.871

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

GnomAD4 genome AF: 0.873 AC: 132863 AN: 152242 Hom.: 58385 Cov.: 31 AF XY: 0.873 AC XY: 64974 AN XY: 74450

Gnomad4 AFR AF: 0.948

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.851

Gnomad4 OTH AF: 0.873

Alfa AF: 0.852 Hom.: 48946

Bravo AF: 0.861

Asia WGS AF: 0.923 AC: 3212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2592991; hg19: chr9-88000506;