rs10494686

Variant names:

• chr1-193482710-G-C
• rs10494686
• ENST00000691564.2:n.201G>C

Variant summary

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

The ENST00000691564.2(ENSG00000286285):​n.201G>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 0.0805 in 152,196 control chromosomes in the GnomAD database, including 1,145 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 0.080 (1145 hom., cov: 32)
• Consequence: ENSG00000286285 ENST00000691564.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 0 publications found

Genes affected

ENSG00000286285 (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 (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691564.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286285	ENST00000691564.2		n.201G>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000286285	ENST00000767718.1		n.175G>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000227240	ENST00000656143.2		n.153+9334G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0804 AC: 12229 AN: 152078 Hom.: 1141 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0752

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0533

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.00791

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0805 AC: 12245 AN: 152196 Hom.: 1145 Cov.: 32 AF XY: 0.0816 AC XY: 6072 AN XY: 74434

African (AFR) AF: 0.218 AC: 9031 AN: 41490

American (AMR) AF: 0.0751 AC: 1148 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0582 AC: 202 AN: 3470

East Asian (EAS) AF: 0.172 AC: 892 AN: 5172

South Asian (SAS) AF: 0.0531 AC: 256 AN: 4820

European-Finnish (FIN) AF: 0.00235 AC: 25 AN: 10618

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.00791 AC: 538 AN: 68012

Other (OTH) AF: 0.0592 AC: 125 AN: 2112

Alfa AF: 0.0472 Hom.: 77

Bravo AF: 0.0954

Asia WGS AF: 0.0970 AC: 337 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	0.70
DANN	Benign	0.26
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs10494686; hg19: chr1-193451840;