1-186716686-C-A

Variant names:

• chr1-186716686-C-A
• rs6685280
• ENST00000742757.1:n.142+5717C>A

Variant summary

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

The ENST00000742757.1(ENSG00000296822):​n.142+5717C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,140 control chromosomes in the GnomAD database, including 43,018 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 0.75 (43018 hom., cov: 33)
• Consequence: ENSG00000296822 ENST00000742757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 5 publications found

Genes affected

ENSG00000296822 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000742757.1. 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
	ENSG00000296822	ENST00000742757.1		n.142+5717C>A		intron	N/A
	ENSG00000296822	ENST00000742758.1		n.190+169C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113617 AN: 152022 Hom.: 43010 Cov.: 33

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.949

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.747 AC: 113650 AN: 152140 Hom.: 43018 Cov.: 33 AF XY: 0.753 AC XY: 55979 AN XY: 74382

African (AFR) AF: 0.622 AC: 25773 AN: 41458

American (AMR) AF: 0.802 AC: 12253 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2572 AN: 3470

East Asian (EAS) AF: 0.950 AC: 4928 AN: 5190

South Asian (SAS) AF: 0.740 AC: 3569 AN: 4824

European-Finnish (FIN) AF: 0.831 AC: 8803 AN: 10592

Middle Eastern (MID) AF: 0.753 AC: 220 AN: 292

European-Non Finnish (NFE) AF: 0.783 AC: 53225 AN: 68006

Other (OTH) AF: 0.742 AC: 1568 AN: 2112

Alfa AF: 0.762 Hom.: 117631

Bravo AF: 0.741

Asia WGS AF: 0.793 AC: 2757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.19
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs6685280; hg19: chr1-186685818; COSMIC: COSV59997195;