rs1033465

Positions:

• chr1-173018590-T-A
• chr1-173018590-T-C
• chr1-173018590-T-G

Variant summary

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

The ENST00000432694.2(ENSG00000224228):​n.589+2066T>A 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 0.951 in 152,300 control chromosomes in the GnomAD database, including 69,002 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 0.95 (69002 hom., cov: 32)
• Consequence: ENST00000432694.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.29

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.979 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
	ENST00000432694.2	n.589+2066T>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.951 AC: 144700 AN: 152182 Hom.: 68959 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.961

Gnomad ASJ AF: 0.963

Gnomad EAS AF: 0.966

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.978

Gnomad NFE AF: 0.985

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.951 AC: 144800 AN: 152300 Hom.: 69002 Cov.: 32 AF XY: 0.951 AC XY: 70776 AN XY: 74454

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.961

Gnomad4 ASJ AF: 0.963

Gnomad4 EAS AF: 0.966

Gnomad4 SAS AF: 0.911

Gnomad4 FIN AF: 0.989

Gnomad4 NFE AF: 0.985

Gnomad4 OTH AF: 0.954

Alfa AF: 0.967 Hom.: 8304

Bravo AF: 0.947

Asia WGS AF: 0.925 AC: 3217 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.081
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1033465; hg19: chr1-172987730;