5-57883677-T-C

Variant names:

• chr5-57883677-T-C
• rs1020661
• ENST00000761558.1:n.148+6898T>C

Variant summary

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

The ENST00000761558.1(ENSG00000299201):​n.148+6898T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.629 in 152,060 control chromosomes in the GnomAD database, including 30,393 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 0.63 (30393 hom., cov: 32)
• Consequence: ENSG00000299201 ENST00000761558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 5 publications found

Genes affected

ENSG00000299201 (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 (SAS) allele frequency at 95% confidence interval = 0.693 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
ENSG00000299201	ENST00000761558.1	n.148+6898T>C		intron_variant	Intron 2 of 3
ENSG00000299201	ENST00000761559.1	n.53-6688T>C		intron_variant	Intron 1 of 3
ENSG00000299201	ENST00000761560.1	n.53+11339T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95667 AN: 151942 Hom.: 30396 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.834

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.629 AC: 95684 AN: 152060 Hom.: 30393 Cov.: 32 AF XY: 0.630 AC XY: 46810 AN XY: 74312

African (AFR) AF: 0.593 AC: 24591 AN: 41482

American (AMR) AF: 0.514 AC: 7858 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.715 AC: 2483 AN: 3472

East Asian (EAS) AF: 0.638 AC: 3295 AN: 5168

South Asian (SAS) AF: 0.712 AC: 3427 AN: 4810

European-Finnish (FIN) AF: 0.660 AC: 6976 AN: 10564

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44782 AN: 67970

Other (OTH) AF: 0.623 AC: 1317 AN: 2114

Alfa AF: 0.645 Hom.: 123298

Bravo AF: 0.613

Asia WGS AF: 0.630 AC: 2195 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	1.0
DANN	Benign	0.24
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs1020661; hg19: chr5-57179504;