1-86502901-C-G

Variant names:

• chr1-86502901-C-G
• rs2791480
• ENST00000760295.1:n.123G>C

Variant summary

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

The ENST00000760295.1(ENSG00000299069):​n.123G>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 0.723 in 152,006 control chromosomes in the GnomAD database, including 39,896 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 0.72 (39896 hom., cov: 31)
• Consequence: ENSG00000299069 ENST00000760295.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 2 publications found

Genes affected

ENSG00000299069 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378827	XR_001738132.2	n.145G>C		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105378827	XR_947557.2	n.404G>C		non_coding_transcript_exon_variant	Exon 2 of 2
LOC124904210	XR_007066206.1	n.226-22093G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299069	ENST00000760295.1	n.123G>C		non_coding_transcript_exon_variant	Exon 2 of 5
ENSG00000299069	ENST00000760296.1	n.242G>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000299069	ENST00000760297.1	n.145G>C		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000299045	ENST00000760090.1	n.26+12C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109821 AN: 151888 Hom.: 39873 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.723 AC: 109888 AN: 152006 Hom.: 39896 Cov.: 31 AF XY: 0.721 AC XY: 53590 AN XY: 74290

African (AFR) AF: 0.671 AC: 27828 AN: 41484

American (AMR) AF: 0.711 AC: 10858 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2363 AN: 3468

East Asian (EAS) AF: 0.704 AC: 3614 AN: 5132

South Asian (SAS) AF: 0.793 AC: 3822 AN: 4818

European-Finnish (FIN) AF: 0.680 AC: 7187 AN: 10566

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.761 AC: 51708 AN: 67966

Other (OTH) AF: 0.706 AC: 1482 AN: 2100

Alfa AF: 0.735 Hom.: 4838

Bravo AF: 0.720

Asia WGS AF: 0.738 AC: 2570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs2791480; hg19: chr1-86968584; COSMIC: COSV52326399;