rs12131057

chr1-38158457-G-A

Variant summary

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

The ENST00000655033.1(ENSG00000286552):n.636-3236G>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 0.198 in 151,998 control chromosomes in the GnomAD database, including 3,337 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 0.20 (3337 hom., cov: 31)
• Consequence: ENST00000655033.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.344

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378654	XR_007065910.1	n.220-3236G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000655033.1	n.636-3236G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30086 AN: 151880 Hom.: 3334 Cov.: 31

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0124

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.198 AC: 30102 AN: 151998 Hom.: 3337 Cov.: 31 AF XY: 0.198 AC XY: 14686 AN XY: 74304

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.261

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.218

Alfa AF: 0.229 Hom.: 5459

Bravo AF: 0.183

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.6
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12131057; hg19: chr1-38624129;