1-17876886-C-G

Variant names:

• chr1-17876886-C-G
• rs578987
• ENST00000737018.1:n.1035G>C

Variant summary

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

The ENST00000737018.1(ENSG00000296161):​n.1035G>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 0.734 in 151,790 control chromosomes in the GnomAD database, including 41,152 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 0.73 (41152 hom., cov: 30)
• Consequence: ENSG00000296161 ENST00000737018.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 2 publications found

Genes affected

ENSG00000296161 (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 (EAS) allele frequency at 95% confidence interval = 0.863 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
ENSG00000296161	ENST00000737018.1	n.1035G>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000296176	ENST00000737115.1	n.397-1929C>G		intron_variant	Intron 2 of 2
ENSG00000296176	ENST00000737116.1	n.444-460C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111319 AN: 151672 Hom.: 41112 Cov.: 30

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.643

Gnomad AMR AF: 0.727

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.763

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.734 AC: 111424 AN: 151790 Hom.: 41152 Cov.: 30 AF XY: 0.735 AC XY: 54527 AN XY: 74160

African (AFR) AF: 0.793 AC: 32802 AN: 41390

American (AMR) AF: 0.728 AC: 11104 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2116 AN: 3472

East Asian (EAS) AF: 0.885 AC: 4522 AN: 5110

South Asian (SAS) AF: 0.734 AC: 3520 AN: 4796

European-Finnish (FIN) AF: 0.763 AC: 8019 AN: 10514

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47120 AN: 67940

Other (OTH) AF: 0.702 AC: 1476 AN: 2104

Alfa AF: 0.645 Hom.: 2122

Bravo AF: 0.735

Asia WGS AF: 0.808 AC: 2812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.10
DANN	Benign	0.37
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs578987; hg19: chr1-18203380; COSMIC: COSV59928138;