rs659235

Variant names:

• chr1-160189366-G-A
• rs659235
• ENST00000799012.1:n.268-242C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-160189366-G-A
• chr1-160189366-G-T

Variant summary

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

The ENST00000799012.1(ENSG00000304031):​n.268-242C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 148,516 control chromosomes in the GnomAD database, including 1,672 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 (1672 hom., cov: 30)
• Consequence: ENSG00000304031 ENST00000799012.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 4 publications found

Genes affected

ENSG00000304031 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000799012.1. 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
	ENSG00000304031	ENST00000799012.1		n.268-242C>T		intron	N/A
	ENSG00000304031	ENST00000799013.1		n.70+3773C>T		intron	N/A
	ENSG00000304031	ENST00000799014.1		n.307-242C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22030 AN: 148396 Hom.: 1670 Cov.: 30

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.148 AC: 22052 AN: 148516 Hom.: 1672 Cov.: 30 AF XY: 0.148 AC XY: 10688 AN XY: 72222

African (AFR) AF: 0.140 AC: 5697 AN: 40564

American (AMR) AF: 0.102 AC: 1492 AN: 14586

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 438 AN: 3432

East Asian (EAS) AF: 0.111 AC: 547 AN: 4932

South Asian (SAS) AF: 0.162 AC: 735 AN: 4538

European-Finnish (FIN) AF: 0.179 AC: 1805 AN: 10104

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 10878 AN: 67134

Other (OTH) AF: 0.129 AC: 262 AN: 2032

Alfa AF: 0.144 Hom.: 2974

Bravo AF: 0.138

Asia WGS AF: 0.136 AC: 472 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.0
DANN	Benign	0.66
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs659235; hg19: chr1-160159156;