chr1-47559391-C-A

Variant names:

• chr1-47559391-C-A
• rs685001
• ENST00000846342.1:n.139+236C>A

Variant summary

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

The ENST00000846342.1(ENSG00000309980):​n.139+236C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 151,920 control chromosomes in the GnomAD database, including 25,806 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 0.57 (25806 hom., cov: 31)
• Consequence: ENSG00000309980 ENST00000846342.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 5 publications found

Genes affected

ENSG00000309980 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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
ENSG00000309980	ENST00000846342.1	n.139+236C>A		intron_variant	Intron 1 of 1
ENSG00000309980	ENST00000846343.1	n.139+221C>A		intron_variant	Intron 1 of 1
ENSG00000309980	ENST00000846344.1	n.83-218C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.566 AC: 85906 AN: 151802 Hom.: 25749 Cov.: 31

Gnomad AFR AF: 0.714

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.566 AC: 86023 AN: 151920 Hom.: 25806 Cov.: 31 AF XY: 0.572 AC XY: 42417 AN XY: 74220

African (AFR) AF: 0.714 AC: 29585 AN: 41418

American (AMR) AF: 0.590 AC: 9013 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1489 AN: 3466

East Asian (EAS) AF: 0.959 AC: 4941 AN: 5150

South Asian (SAS) AF: 0.641 AC: 3083 AN: 4810

European-Finnish (FIN) AF: 0.520 AC: 5491 AN: 10568

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30647 AN: 67922

Other (OTH) AF: 0.531 AC: 1118 AN: 2106

Alfa AF: 0.508 Hom.: 36984

Bravo AF: 0.578

Asia WGS AF: 0.788 AC: 2738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.011
DANN	Benign	0.58
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs685001; hg19: chr1-48025063;