rs1358753

Variant names:

• chr6-160669538-C-G
• rs1358753
• ENST00000452651.1:n.115-3165G>C

Variant summary

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

The ENST00000452651.1(ENSG00000243831):​n.115-3165G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,220 control chromosomes in the GnomAD database, including 1,747 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 (1747 hom., cov: 32)
• Consequence: ENSG00000243831 ENST00000452651.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 6 publications found

Genes affected

ENSG00000243831 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.202 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
ENSG00000243831	ENST00000452651.1	n.115-3165G>C		intron_variant	Intron 1 of 1	6
ENSG00000303834	ENST00000797429.1	n.219-1235G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22089 AN: 152102 Hom.: 1746 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.0901

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.145 AC: 22123 AN: 152220 Hom.: 1747 Cov.: 32 AF XY: 0.141 AC XY: 10503 AN XY: 74412

African (AFR) AF: 0.206 AC: 8547 AN: 41522

American (AMR) AF: 0.122 AC: 1870 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3468

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5182

South Asian (SAS) AF: 0.0842 AC: 406 AN: 4824

European-Finnish (FIN) AF: 0.0901 AC: 956 AN: 10608

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.138 AC: 9389 AN: 68006

Other (OTH) AF: 0.125 AC: 264 AN: 2108

Alfa AF: 0.138 Hom.: 194

Bravo AF: 0.149

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.33
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1358753; hg19: chr6-161090570;