chr17-5898011-G-A

Variant names:

• chr17-5898011-G-A
• rs7221818
• ENST00000573619.1:c.-381+9181G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000573619.1(ENSG00000285471):​c.-381+9181G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,092 control chromosomes in the GnomAD database, including 33,883 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 0.66 (33883 hom., cov: 32)
• Consequence: ENSG00000285471 ENST00000573619.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 6 publications found

Genes affected

ENSG00000285471 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC339166	NR_040000.1	n.904+9181G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285471	ENST00000573619.1	c.-381+9181G>A		intron_variant	Intron 3 of 4	2		ENSP00000461865.1
ENSG00000284837	ENST00000563763.5	n.904+9181G>A		intron_variant	Intron 3 of 3	1

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100762 AN: 151974 Hom.: 33845 Cov.: 32

Gnomad AFR AF: 0.750

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.824

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.663 AC: 100845 AN: 152092 Hom.: 33883 Cov.: 32 AF XY: 0.664 AC XY: 49341 AN XY: 74342

African (AFR) AF: 0.750 AC: 31094 AN: 41468

American (AMR) AF: 0.531 AC: 8116 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2525 AN: 3470

East Asian (EAS) AF: 0.823 AC: 4268 AN: 5184

South Asian (SAS) AF: 0.688 AC: 3312 AN: 4816

European-Finnish (FIN) AF: 0.644 AC: 6814 AN: 10576

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42490 AN: 67982

Other (OTH) AF: 0.659 AC: 1389 AN: 2108

Alfa AF: 0.641 Hom.: 48703

Bravo AF: 0.658

Asia WGS AF: 0.728 AC: 2532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.18
DANN	Benign	0.30
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs7221818; hg19: chr17-5801331;