rs1175152

chr1-192244106-G-A

Variant summary

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

The ENST00000643151.1(ENSG00000285280):n.306-4316C>T 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 0.473 in 151,898 control chromosomes in the GnomAD database, including 17,959 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 0.47 (17959 hom., cov: 32)
• Consequence: ENST00000643151.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000643151.1	n.306-4316C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71846 AN: 151780 Hom.: 17933 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.473 AC: 71911 AN: 151898 Hom.: 17959 Cov.: 32 AF XY: 0.473 AC XY: 35095 AN XY: 74214

Gnomad4 AFR AF: 0.619

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.434

Gnomad4 OTH AF: 0.435

Alfa AF: 0.452 Hom.: 1995

Bravo AF: 0.463

Asia WGS AF: 0.385 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.5
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1175152; hg19: chr1-192213236;