rs2841453

Positions:

• chr9-85399960-G-A
• chr9-85399960-G-C
• chr9-85399960-G-T

Variant summary

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

The ENST00000669133.1(ENSG00000285634):​n.282+2587C>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 0.677 in 152,030 control chromosomes in the GnomAD database, including 36,010 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 0.68 (36010 hom., cov: 32)
• Consequence: ENST00000669133.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 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.282+2587C>T		intron_variant, non_coding_transcript_variant
	ENST00000648131.1	n.600+1725C>T		intron_variant, non_coding_transcript_variant
	ENST00000662737.1	n.1680+1495C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102876 AN: 151912 Hom.: 36008 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.677 AC: 102920 AN: 152030 Hom.: 36010 Cov.: 32 AF XY: 0.677 AC XY: 50264 AN XY: 74292

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.833

Gnomad4 SAS AF: 0.670

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.712

Alfa AF: 0.726 Hom.: 8631

Bravo AF: 0.657

Asia WGS AF: 0.708 AC: 2460 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2841453; hg19: chr9-88014875;