rs4759042

Variant names:

• chr12-56983563-C-T
• rs4759042
• ENST00000611536.1:n.530G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

Genes affected

ENSG00000278399 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611536.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000278399	ENST00000611536.1	TSL:6	n.530G>A		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000303268	ENST00000793297.1		n.100-1674C>T		intron	N/A
	ENSG00000303268	ENST00000793298.1		n.234+300C>T		intron	N/A

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

African (AFR) AF: 0.146 AC: 7 AN: 48

American (AMR) AF: 0.348 AC: 23 AN: 66

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.150 AC: 12 AN: 80

South Asian (SAS) AF: 0.242 AC: 172 AN: 712

European-Finnish (FIN) AF: 0.337 AC: 3375 AN: 10020

Middle Eastern (MID) AF: 0.120 AC: 19 AN: 158

European-Non Finnish (NFE) AF: 0.329 AC: 274 AN: 832

Other (OTH) AF: 0.304 AC: 59 AN: 194

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

African (AFR) AF: 0.149 AC: 6164 AN: 41482

American (AMR) AF: 0.314 AC: 4795 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.247 AC: 855 AN: 3466

East Asian (EAS) AF: 0.160 AC: 828 AN: 5166

South Asian (SAS) AF: 0.259 AC: 1246 AN: 4818

European-Finnish (FIN) AF: 0.346 AC: 3658 AN: 10580

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23394 AN: 67956

Other (OTH) AF: 0.252 AC: 532 AN: 2112

Alfa AF: 0.316 Hom.: 23968

Bravo AF: 0.270

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.9
DANN	Benign	0.57
PhyloP100		2.7

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: rs4759042;

hg19: chr12-57377347;