chr1-5650383-T-C

Variant names:

• chr1-5650383-T-C
• rs707586
• ENST00000413887.1:n.155+17758A>G

Variant summary

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

The ENST00000413887.1(ENSG00000289893):​n.155+17758A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 151,980 control chromosomes in the GnomAD database, including 1,890 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 0.15 (1890 hom., cov: 32)
• Consequence: ENSG00000289893 ENST00000413887.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.778
• Publications: 3 publications found

Genes affected

ENSG00000289893 (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 = 0.275 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000413887.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289893	ENST00000413887.1	TSL:5	n.155+17758A>G		intron	N/A
	ENSG00000289893	ENST00000637702.1	TSL:2	n.115+17758A>G		intron	N/A
	ENSG00000289893	ENST00000727750.1		n.188-71342A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23349 AN: 151858 Hom.: 1886 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.0474

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.0892

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.154 AC: 23369 AN: 151980 Hom.: 1890 Cov.: 32 AF XY: 0.153 AC XY: 11395 AN XY: 74280

African (AFR) AF: 0.166 AC: 6867 AN: 41452

American (AMR) AF: 0.134 AC: 2050 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3468

East Asian (EAS) AF: 0.287 AC: 1475 AN: 5140

South Asian (SAS) AF: 0.170 AC: 820 AN: 4810

European-Finnish (FIN) AF: 0.113 AC: 1197 AN: 10584

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.147 AC: 9969 AN: 67946

Other (OTH) AF: 0.126 AC: 265 AN: 2104

Alfa AF: 0.150 Hom.: 282

Bravo AF: 0.155

Asia WGS AF: 0.226 AC: 786 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	0.42
DANN	Benign	0.62
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs707586; hg19: chr1-5710443;