18-71203777-G-C

Variant names:

• chr18-71203777-G-C
• rs4439856
• ENST00000658819.1:n.1131G>C

Variant summary

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

The ENST00000658819.1(ENSG00000287693):​n.1131G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 151,988 control chromosomes in the GnomAD database, including 35,257 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 0.67 (35257 hom., cov: 32)
• Consequence: ENSG00000287693 ENST00000658819.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720
• Publications: 2 publications found

Genes affected

ENSG00000287693 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658819.1. 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
	ENSG00000287693	ENST00000658819.1		n.1131G>C		non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.674 AC: 102313 AN: 151870 Hom.: 35266 Cov.: 32

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.673 AC: 102329 AN: 151988 Hom.: 35257 Cov.: 32 AF XY: 0.674 AC XY: 50077 AN XY: 74284

African (AFR) AF: 0.537 AC: 22220 AN: 41416

American (AMR) AF: 0.723 AC: 11055 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2975 AN: 3472

East Asian (EAS) AF: 0.638 AC: 3277 AN: 5138

South Asian (SAS) AF: 0.721 AC: 3467 AN: 4810

European-Finnish (FIN) AF: 0.706 AC: 7466 AN: 10572

Middle Eastern (MID) AF: 0.853 AC: 249 AN: 292

European-Non Finnish (NFE) AF: 0.727 AC: 49449 AN: 67974

Other (OTH) AF: 0.692 AC: 1462 AN: 2112

Alfa AF: 0.692 Hom.: 4596

Bravo AF: 0.670

Asia WGS AF: 0.654 AC: 2276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.37
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs4439856; hg19: chr18-68871013;