rs12724719

chr1-156693719-G-A

Variant summary

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

The ENST00000650347.1(ENSG00000285570):n.149+3895G>A 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 0.17 in 151,948 control chromosomes in the GnomAD database, including 2,377 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 0.17 (2377 hom., cov: 31)
• Consequence: ENST00000650347.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

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 (AMR) allele frequency at 95% confidence interval = 0.252 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
	ENST00000650347.1	n.149+3895G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25853 AN: 151830 Hom.: 2373 Cov.: 31

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.0671

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.170 AC: 25881 AN: 151948 Hom.: 2377 Cov.: 31 AF XY: 0.172 AC XY: 12755 AN XY: 74226

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.258

Gnomad4 ASJ AF: 0.0671

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.169

Alfa AF: 0.164 Hom.: 850

Bravo AF: 0.181

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.058
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12724719; hg19: chr1-156663511;