rs1566037

Variant names:

• chr5-26666753-C-A
• rs1566037
• ENST00000752444.1:n.341+7657C>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000752444.1(ENSG00000298005):​n.341+7657C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,932 control chromosomes in the GnomAD database, including 9,205 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 0.28 (9205 hom., cov: 32)
• Consequence: ENSG00000298005 ENST00000752444.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54
• Publications: 2 publications found

Genes affected

ENSG00000298005 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.597 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
ENSG00000298005	ENST00000752444.1	n.341+7657C>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43103 AN: 151812 Hom.: 9177 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.284 AC: 43176 AN: 151932 Hom.: 9205 Cov.: 32 AF XY: 0.280 AC XY: 20804 AN XY: 74240

African (AFR) AF: 0.604 AC: 25017 AN: 41450

American (AMR) AF: 0.217 AC: 3315 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 428 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1023 AN: 5166

South Asian (SAS) AF: 0.264 AC: 1274 AN: 4824

European-Finnish (FIN) AF: 0.146 AC: 1541 AN: 10548

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9913 AN: 67892

Other (OTH) AF: 0.243 AC: 514 AN: 2112

Alfa AF: 0.213 Hom.: 1941

Bravo AF: 0.300

Asia WGS AF: 0.277 AC: 961 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	9.2
DANN	Benign	0.59
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1566037; hg19: chr5-26666862;