rs677618

Variant names:

• chr1-181857976-C-T
• rs677618
• ENST00000717053.1:n.288-22340G>A

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.288-22340G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.762 in 152,068 control chromosomes in the GnomAD database, including 44,751 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 0.76 (44751 hom., cov: 31)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.419
• Publications: 4 publications found

Genes affected

ENSG00000287452 (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 (AFR) allele frequency at 95% confidence interval = 0.875 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
ENSG00000287452	ENST00000717053.1	n.288-22340G>A		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717054.1	n.293-22340G>A		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717055.1	n.81-22340G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115852 AN: 151950 Hom.: 44706 Cov.: 31

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.762 AC: 115946 AN: 152068 Hom.: 44751 Cov.: 31 AF XY: 0.760 AC XY: 56506 AN XY: 74318

African (AFR) AF: 0.883 AC: 36637 AN: 41496

American (AMR) AF: 0.744 AC: 11365 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.628 AC: 2181 AN: 3472

East Asian (EAS) AF: 0.656 AC: 3384 AN: 5162

South Asian (SAS) AF: 0.742 AC: 3580 AN: 4826

European-Finnish (FIN) AF: 0.735 AC: 7769 AN: 10568

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.714 AC: 48500 AN: 67954

Other (OTH) AF: 0.758 AC: 1604 AN: 2116

Alfa AF: 0.726 Hom.: 80634

Bravo AF: 0.768

Asia WGS AF: 0.701 AC: 2438 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	1.2
DANN	Benign	0.41
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs677618; hg19: chr1-181827111;