rs12037606

Positions:

• chr1-172929262-G-A

Variant summary

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

The ENST00000432694.2(ENSG00000224228):​n.224-75020G>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 0.525 in 151,730 control chromosomes in the GnomAD database, including 22,349 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 0.53 (22349 hom., cov: 33)
• Consequence: ENST00000432694.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 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
	ENST00000432694.2	n.224-75020G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.525 AC: 79629 AN: 151612 Hom.: 22325 Cov.: 33

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.919

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.529

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

GnomAD4 genome AF: 0.525 AC: 79705 AN: 151730 Hom.: 22349 Cov.: 33 AF XY: 0.536 AC XY: 39757 AN XY: 74134

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.919

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.528

Alfa AF: 0.446 Hom.: 17987

Bravo AF: 0.544

Asia WGS AF: 0.727 AC: 2526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12037606; hg19: chr1-172898402;