2-1546537-T-C

Position:

• chr2-1546537-T-C

Variant summary

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

The variant allele was found at a frequency of 0.685 in 152,076 control chromosomes in the GnomAD database, including 35,904 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 0.68 (35900 hom., cov: 32)
  • Exomes 𝑓: 0.64 (4 hom.)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.1546537T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000231482	ENST00000650512.1	n.547+33664A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.685 AC: 104004 AN: 151936 Hom.: 35841 Cov.: 32

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.670

GnomAD4 exome AF: 0.636 AC: 14 AN: 22 Hom.: 4 AF XY: 0.500 AC XY: 7 AN XY: 14

Gnomad4 FIN exome AF: 0.625

Gnomad4 NFE exome AF: 0.700

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.685 AC: 104127 AN: 152054 Hom.: 35900 Cov.: 32 AF XY: 0.684 AC XY: 50818 AN XY: 74330

Gnomad4 AFR AF: 0.781

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.657

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.676

Alfa AF: 0.651 Hom.: 5985

Bravo AF: 0.688

Asia WGS AF: 0.664 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.5
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6705087; hg19: chr2-1550309;