rs4759042

Positions:

• chr12-56983563-C-T

Variant summary

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

The ENST00000611536.1(ENSG00000278399):​n.530G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 164,178 control chromosomes in the GnomAD database, including 7,126 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 0.27 (6437 hom., cov: 31)
  • Exomes 𝑓: 0.33 (689 hom.)
• Consequence: ENSG00000278399 ENST00000611536.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.73

Genes affected

ENSG00000278399 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC390332		n.56983563C>T		intragenic_variant
LOC124902945	XR_007063332.1	n.1336-2136G>A		intron_variant
LOC124902945	XR_007063333.1	n.293-2136G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000278399	ENST00000611536.1	n.530G>A		non_coding_transcript_exon_variant	2/4	6

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41729 AN: 151948 Hom.: 6427 Cov.: 31

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.254

GnomAD4 exome AF: 0.325 AC: 3941 AN: 12112 Hom.: 689 Cov.: 0 AF XY: 0.321 AC XY: 1905 AN XY: 5926

Gnomad4 AFR exome AF: 0.146

Gnomad4 AMR exome AF: 0.348

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.150

Gnomad4 SAS exome AF: 0.242

Gnomad4 FIN exome AF: 0.337

Gnomad4 NFE exome AF: 0.329

Gnomad4 OTH exome AF: 0.304

GnomAD4 genome AF: 0.274 AC: 41742 AN: 152066 Hom.: 6437 Cov.: 31 AF XY: 0.273 AC XY: 20276 AN XY: 74314

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.344

Gnomad4 OTH AF: 0.252

Alfa AF: 0.319 Hom.: 9308

Bravo AF: 0.270

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.9
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4759042; hg19: chr12-57377347;