rs1558557

Variant names:

• chr7-8269363-G-A
• rs1558557
• ENST00000424460.1:n.493+4683G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-8269363-G-A
• chr7-8269363-G-C
• chr7-8269363-G-T

Variant summary

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

The ENST00000424460.1(ENSG00000229970):​n.493+4683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,070 control chromosomes in the GnomAD database, including 15,946 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 0.46 (15946 hom., cov: 32)
• Consequence: ENSG00000229970 ENST00000424460.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 7 publications found

Genes affected

ENSG00000229970 (HGNC:):

ICA1-AS1 (HGNC:55606): (ICA1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ICA1-AS1	NR_125740.1	n.532+4683G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000229970	ENST00000424460.1	n.493+4683G>A		intron_variant	Intron 3 of 6	5
ICA1-AS1	ENST00000716350.1	n.*82G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69421 AN: 151952 Hom.: 15939 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.457 AC: 69452 AN: 152070 Hom.: 15946 Cov.: 32 AF XY: 0.452 AC XY: 33580 AN XY: 74326

African (AFR) AF: 0.422 AC: 17492 AN: 41464

American (AMR) AF: 0.470 AC: 7185 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1708 AN: 3468

East Asian (EAS) AF: 0.564 AC: 2924 AN: 5180

South Asian (SAS) AF: 0.352 AC: 1696 AN: 4812

European-Finnish (FIN) AF: 0.493 AC: 5202 AN: 10552

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.466 AC: 31660 AN: 67986

Other (OTH) AF: 0.483 AC: 1021 AN: 2114

Alfa AF: 0.465 Hom.: 48962

Bravo AF: 0.460

Asia WGS AF: 0.436 AC: 1519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.7
DANN	Benign	0.74
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1558557; hg19: chr7-8308993;