chr5-51633037-A-G

Variant names:

• chr5-51633037-A-G
• rs244545
• ENST00000666280.1:n.435+31577T>C

Variant summary

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

The ENST00000666280.1(ENSG00000288035):​n.435+31577T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 151,948 control chromosomes in the GnomAD database, including 36,142 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 0.68 (36142 hom., cov: 31)
• Consequence: ENSG00000288035 ENST00000666280.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.742
• Publications: 4 publications found

Genes affected

ENSG00000288035 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.849 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
ENSG00000288035	ENST00000666280.1	n.435+31577T>C		intron_variant	Intron 1 of 3
ENSG00000288035	ENST00000730931.1	n.110+31577T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102812 AN: 151830 Hom.: 36102 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.677 AC: 102899 AN: 151948 Hom.: 36142 Cov.: 31 AF XY: 0.671 AC XY: 49798 AN XY: 74228

African (AFR) AF: 0.857 AC: 35526 AN: 41476

American (AMR) AF: 0.601 AC: 9175 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2439 AN: 3472

East Asian (EAS) AF: 0.334 AC: 1724 AN: 5162

South Asian (SAS) AF: 0.600 AC: 2887 AN: 4810

European-Finnish (FIN) AF: 0.588 AC: 6175 AN: 10508

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.629 AC: 42705 AN: 67944

Other (OTH) AF: 0.647 AC: 1362 AN: 2106

Alfa AF: 0.644 Hom.: 92690

Bravo AF: 0.682

Asia WGS AF: 0.477 AC: 1657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	12
DANN	Benign	0.57
PhyloP100		0.74

Splicing

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

Other links and lift over

dbSNP: rs244545; hg19: chr5-50928871;