12-93156525-G-T

Variant names:

• chr12-93156525-G-T
• rs1836127
• ENST00000549930.1:n.98+59057C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_040096.1(LOC643339):​n.427+59057C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 151,902 control chromosomes in the GnomAD database, including 11,163 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 0.38 (11163 hom., cov: 31)
• Consequence: LOC643339 NR_040096.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 11 publications found

Genes affected

ENSG00000257252 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_040096.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC643339	NR_040096.1		n.427+59057C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257252	ENST00000549930.1	TSL:5	n.98+59057C>A		intron	N/A
	ENSG00000257252	ENST00000754393.1		n.766+33742C>A		intron	N/A
	ENSG00000257252	ENST00000754394.1		n.715+33742C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58041 AN: 151784 Hom.: 11141 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.404

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

GnomAD4 genome AF: 0.382 AC: 58102 AN: 151902 Hom.: 11163 Cov.: 31 AF XY: 0.387 AC XY: 28738 AN XY: 74228

African (AFR) AF: 0.346 AC: 14315 AN: 41430

American (AMR) AF: 0.446 AC: 6797 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1328 AN: 3470

East Asian (EAS) AF: 0.320 AC: 1658 AN: 5176

South Asian (SAS) AF: 0.469 AC: 2255 AN: 4812

European-Finnish (FIN) AF: 0.422 AC: 4451 AN: 10536

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25905 AN: 67926

Other (OTH) AF: 0.401 AC: 843 AN: 2104

Alfa AF: 0.384 Hom.: 52579

Bravo AF: 0.379

Asia WGS AF: 0.410 AC: 1429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.046
DANN	Benign	0.55
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1836127; hg19: chr12-93550301;