rs12092383

Positions:

• chr1-173607581-G-A
• chr1-173607581-G-C
• chr1-173607581-G-T

Variant summary

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

The ENST00000431459.1(ENSG00000238272):​n.528+4350G>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 0.424 in 152,002 control chromosomes in the GnomAD database, including 17,261 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 0.42 (17261 hom., cov: 32)
• Consequence: ENST00000431459.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.684

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 = 0.744 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
	ENST00000431459.1	n.528+4350G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.424 AC: 64390 AN: 151882 Hom.: 17201 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.424 AC: 64511 AN: 152002 Hom.: 17261 Cov.: 32 AF XY: 0.418 AC XY: 31083 AN XY: 74290

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.391

Alfa AF: 0.323 Hom.: 4803

Bravo AF: 0.448

Asia WGS AF: 0.442 AC: 1535 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
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: rs12092383; hg19: chr1-173576720;