18-77540028-G-C

Variant names:

• chr18-77540028-G-C
• rs4131672
• ENST00000583629.2:n.497+17106G>C

Variant summary

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

The ENST00000583629.2(ENSG00000264015):​n.497+17106G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 152,028 control chromosomes in the GnomAD database, including 6,396 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 0.26 (6396 hom., cov: 32)
• Consequence: ENSG00000264015 ENST00000583629.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.305
• Publications: 2 publications found

Genes affected

ENSG00000264015 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000583629.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000264015	ENST00000583629.2	TSL:4	n.497+17106G>C		intron	N/A
	ENSG00000264015	ENST00000744289.1		n.270+17106G>C		intron	N/A
	ENSG00000264015	ENST00000744290.1		n.496-73155G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39311 AN: 151908 Hom.: 6388 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0632

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0879

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.259 AC: 39356 AN: 152028 Hom.: 6396 Cov.: 32 AF XY: 0.250 AC XY: 18557 AN XY: 74344

African (AFR) AF: 0.448 AC: 18550 AN: 41406

American (AMR) AF: 0.306 AC: 4669 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3470

East Asian (EAS) AF: 0.0633 AC: 328 AN: 5178

South Asian (SAS) AF: 0.144 AC: 693 AN: 4826

European-Finnish (FIN) AF: 0.0879 AC: 930 AN: 10578

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13028 AN: 67982

Other (OTH) AF: 0.236 AC: 498 AN: 2110

Alfa AF: 0.231 Hom.: 628

Bravo AF: 0.287

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.87
DANN	Benign	0.43
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs4131672; hg19: chr18-75251984;