chr8-60890428-C-G

Variant names:

• chr8-60890428-C-G
• rs4237043
• ENST00000658608.1:n.357+5278C>G

Variant summary

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

The ENST00000658608.1(ENSG00000287975):​n.357+5278C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,176 control chromosomes in the GnomAD database, including 48,380 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 0.80 (48380 hom., cov: 32)
• Consequence: ENSG00000287975 ENST00000658608.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.222
• Publications: 2 publications found

Genes affected

ENSG00000287975 (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 (AMR) allele frequency at 95% confidence interval = 0.824 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
ENSG00000287975	ENST00000658608.1	n.357+5278C>G		intron_variant	Intron 1 of 1
ENSG00000287975	ENST00000668199.1	n.756+5278C>G		intron_variant	Intron 3 of 4
ENSG00000287975	ENST00000829534.1	n.266+5278C>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.796 AC: 121106 AN: 152058 Hom.: 48344 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.796 AC: 121201 AN: 152176 Hom.: 48380 Cov.: 32 AF XY: 0.794 AC XY: 59093 AN XY: 74384

African (AFR) AF: 0.766 AC: 31790 AN: 41510

American (AMR) AF: 0.836 AC: 12796 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2919 AN: 3470

East Asian (EAS) AF: 0.819 AC: 4231 AN: 5164

South Asian (SAS) AF: 0.773 AC: 3722 AN: 4818

European-Finnish (FIN) AF: 0.740 AC: 7834 AN: 10584

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55230 AN: 68012

Other (OTH) AF: 0.806 AC: 1704 AN: 2114

Alfa AF: 0.755 Hom.: 2268

Bravo AF: 0.803

Asia WGS AF: 0.754 AC: 2624 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	0.32
DANN	Benign	0.26
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs4237043; hg19: chr8-61802987;