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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372188	XR_935610.4	n.940G>C		non_coding_transcript_exon_variant	Exon 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287693	ENST00000658819.1	n.1131G>C		non_coding_transcript_exon_variant	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 v4.3

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;