12-5368982-G-T

Variant names:

• chr12-5368982-G-T
• rs10492094
• ENST00000537192.2:n.358+1048G>T

Variant summary

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

The ENST00000537192.2(ENSG00000256417):​n.358+1048G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,988 control chromosomes in the GnomAD database, including 5,266 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 0.23 (5266 hom., cov: 32)
• Consequence: ENSG00000256417 ENST00000537192.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.499
• Publications: 3 publications found

Genes affected

ENSG00000256417 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000537192.2. 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
	LOC105369617	NR_188065.1		n.1234+1048G>T		intron	N/A
	LOC105369617	NR_188066.1		n.1143+1048G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000256417	ENST00000537192.2	TSL:4	n.358+1048G>T		intron	N/A
	ENSG00000256218	ENST00000543308.2	TSL:6	n.597+466C>A		intron	N/A
	ENSG00000256417	ENST00000789688.1		n.820+1048G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35450 AN: 151870 Hom.: 5268 Cov.: 32

Gnomad AFR AF: 0.0613

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.0959

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.233 AC: 35443 AN: 151988 Hom.: 5266 Cov.: 32 AF XY: 0.232 AC XY: 17244 AN XY: 74256

African (AFR) AF: 0.0614 AC: 2544 AN: 41460

American (AMR) AF: 0.222 AC: 3388 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1111 AN: 3468

East Asian (EAS) AF: 0.0954 AC: 493 AN: 5168

South Asian (SAS) AF: 0.228 AC: 1097 AN: 4818

European-Finnish (FIN) AF: 0.304 AC: 3199 AN: 10522

Middle Eastern (MID) AF: 0.281 AC: 82 AN: 292

European-Non Finnish (NFE) AF: 0.334 AC: 22716 AN: 67972

Other (OTH) AF: 0.256 AC: 539 AN: 2106

Alfa AF: 0.283 Hom.: 15270

Bravo AF: 0.216

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.59
PhyloP100		0.50

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10492094;

hg19: chr12-5478148;