rs758216

Variant names:

• chr1-230563488-T-A
• rs758216
• ENST00000685406.1:n.242-13006T>A

Your query was ambiguous. Multiple possible variants found:

• chr1-230563488-T-A
• chr1-230563488-T-C

Variant summary

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

The ENST00000685406.1(ENSG00000282564):​n.242-13006T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,230 control chromosomes in the GnomAD database, including 1,565 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 0.13 (1565 hom., cov: 32)
• Consequence: ENSG00000282564 ENST00000685406.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177
• Publications: 2 publications found

Genes affected

ENSG00000282564 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685406.1. 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
	ENSG00000282564	ENST00000685406.1		n.242-13006T>A		intron	N/A
	ENSG00000282564	ENST00000689608.2		n.330-55475T>A		intron	N/A
	ENSG00000282564	ENST00000692577.3		n.319-55475T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19768 AN: 152114 Hom.: 1566 Cov.: 32

Gnomad AFR AF: 0.0972

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.0623

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.130 AC: 19766 AN: 152230 Hom.: 1565 Cov.: 32 AF XY: 0.129 AC XY: 9635 AN XY: 74422

African (AFR) AF: 0.0970 AC: 4031 AN: 41544

American (AMR) AF: 0.128 AC: 1957 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 366 AN: 3472

East Asian (EAS) AF: 0.388 AC: 2008 AN: 5172

South Asian (SAS) AF: 0.249 AC: 1197 AN: 4816

European-Finnish (FIN) AF: 0.0623 AC: 661 AN: 10614

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9116 AN: 68006

Other (OTH) AF: 0.144 AC: 305 AN: 2114

Alfa AF: 0.126 Hom.: 144

Bravo AF: 0.132

Asia WGS AF: 0.317 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.5
DANN	Benign	0.69
PhyloP100		0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs758216;

hg19: chr1-230699234;