12-5368982-G-T

Variant summary

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

The ENST00000537192.1(ENSG00000256417):n.351+1048G>T 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 0.233 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: ENST00000537192.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.499

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105369617	XR_931577.2	n.1231+1048G>T		intron_variant, non_coding_transcript_variant
LOC105369617	XR_001748970.2	n.1130+1048G>T		intron_variant, non_coding_transcript_variant
LOC105369617	XR_007063177.1	n.1104+1048G>T		intron_variant, non_coding_transcript_variant
LOC105369617	XR_007063178.1	n.1187+1048G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000537192.1	n.351+1048G>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.0614

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.0954

Gnomad4 SAS AF: 0.228

Gnomad4 FIN AF: 0.304

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.256

Alfa AF: 0.300 Hom.: 10652

Bravo AF: 0.216

Asia WGS AF: 0.137 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.0
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10492094; hg19: chr12-5478148;