rs2593017

Positions:

• chr9-85395765-T-A
• chr9-85395765-T-C
• chr9-85395765-T-G

Variant summary

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

The ENST00000669133.1(ENSG00000285634):​n.282+6782A>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 0.875 in 152,242 control chromosomes in the GnomAD database, including 58,650 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 0.88 (58650 hom., cov: 32)
• Consequence: ENST00000669133.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000669133.1	n.282+6782A>T		intron_variant, non_coding_transcript_variant
	ENST00000648131.1	n.600+5920A>T		intron_variant, non_coding_transcript_variant
	ENST00000662737.1	n.1680+5690A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.875 AC: 133173 AN: 152124 Hom.: 58607 Cov.: 32

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.904

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.875 AC: 133273 AN: 152242 Hom.: 58650 Cov.: 32 AF XY: 0.876 AC XY: 65170 AN XY: 74422

Gnomad4 AFR AF: 0.949

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.904

Gnomad4 FIN AF: 0.890

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.878

Alfa AF: 0.869 Hom.: 6720

Bravo AF: 0.867

Asia WGS AF: 0.927 AC: 3223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.079
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2593017; hg19: chr9-88010680;