18-77187813-T-G

Variant names:

• chr18-77187813-T-G
• rs1562774
• ENST00000584843.1:n.209+2516T>G

Variant summary

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

The ENST00000584843.1(ENSG00000265844):​n.209+2516T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.979 in 152,146 control chromosomes in the GnomAD database, including 73,020 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 0.98 (73020 hom., cov: 30)
• Consequence: ENSG00000265844 ENST00000584843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• Publications: 1 publications found

Genes affected

ENSG00000265844 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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
ENSG00000265844	ENST00000584843.1	n.209+2516T>G		intron_variant	Intron 2 of 4	4
ENSG00000265844	ENST00000843890.1	n.415-651T>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.979 AC: 148865 AN: 152028 Hom.: 72962 Cov.: 30

Gnomad AFR AF: 0.929

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.991

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 1.00

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.986

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

GnomAD4 genome AF: 0.979 AC: 148982 AN: 152146 Hom.: 73020 Cov.: 30 AF XY: 0.980 AC XY: 72903 AN XY: 74368

African (AFR) AF: 0.929 AC: 38540 AN: 41478

American (AMR) AF: 0.991 AC: 15150 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3427 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5172 AN: 5172

South Asian (SAS) AF: 0.999 AC: 4813 AN: 4816

European-Finnish (FIN) AF: 1.00 AC: 10580 AN: 10580

Middle Eastern (MID) AF: 1.00 AC: 294 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68014 AN: 68032

Other (OTH) AF: 0.986 AC: 2082 AN: 2112

Alfa AF: 0.984 Hom.: 18278

Bravo AF: 0.977

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.69
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1562774; hg19: chr18-74899769;