rs1889022

Variant names:

• chr17-27811330-G-A
• rs1889022
• ENST00000582441.1:c.220-6989C>T

Variant summary

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

The ENST00000582441.1(ENSG00000266202):​c.220-6989C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,028 control chromosomes in the GnomAD database, including 24,089 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 0.54 (24089 hom., cov: 31)
• Consequence: ENSG00000266202 ENST00000582441.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

Genes affected

ENSG00000266202 (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 (EAS) allele frequency at 95% confidence interval = 0.727 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
ENSG00000266202	ENST00000582441.1	c.220-6989C>T		intron_variant	Intron 3 of 4	4		ENSP00000462879.1

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81823 AN: 151910 Hom.: 24093 Cov.: 31

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.634

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.538 AC: 81834 AN: 152028 Hom.: 24089 Cov.: 31 AF XY: 0.544 AC XY: 40417 AN XY: 74320

Gnomad4 AFR AF: 0.283

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.747

Gnomad4 SAS AF: 0.696

Gnomad4 FIN AF: 0.634

Gnomad4 NFE AF: 0.629

Gnomad4 OTH AF: 0.565

Alfa AF: 0.590 Hom.: 7593

Bravo AF: 0.527

Asia WGS AF: 0.679 AC: 2360 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	0.24
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1889022; hg19: chr17-26138356;