rs1358753

Positions:

• chr6-160669538-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000452651.1(ENSG00000243831):​n.115-3165G>C variant causes a intron, non coding transcript 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: ENST00000452651.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000452651.1	n.115-3165G>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.00425

Gnomad4 SAS AF: 0.0842

Gnomad4 FIN AF: 0.0901

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.125

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358753; hg19: chr6-161090570;