rs558370

Variant names:

• chr1-109528491-A-G
• rs558370
• ENST00000819548.1:n.218-840T>C

Variant summary

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

The ENST00000819548.1(ENSG00000306592):​n.218-840T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 151,946 control chromosomes in the GnomAD database, including 27,979 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 0.59 (27979 hom., cov: 31)
• Consequence: ENSG00000306592 ENST00000819548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512
• Publications: 3 publications found

Genes affected

ENSG00000306592 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 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
ENSG00000306592	ENST00000819548.1	n.218-840T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88920 AN: 151828 Hom.: 27936 Cov.: 31

Gnomad AFR AF: 0.830

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.586 AC: 89008 AN: 151946 Hom.: 27979 Cov.: 31 AF XY: 0.580 AC XY: 43083 AN XY: 74232

African (AFR) AF: 0.831 AC: 34417 AN: 41440

American (AMR) AF: 0.433 AC: 6626 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1659 AN: 3468

East Asian (EAS) AF: 0.353 AC: 1822 AN: 5158

South Asian (SAS) AF: 0.599 AC: 2879 AN: 4804

European-Finnish (FIN) AF: 0.480 AC: 5055 AN: 10540

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34631 AN: 67930

Other (OTH) AF: 0.540 AC: 1140 AN: 2112

Alfa AF: 0.558 Hom.: 4316

Bravo AF: 0.588

Asia WGS AF: 0.514 AC: 1789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.43
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs558370; hg19: chr1-110071113;