rs1060236

Variant names:

• chr20-5474040-A-G
• rs1060236
• ENST00000430097.2:n.694A>G

Variant summary

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

The ENST00000430097.2(ENSG00000230563):​n.694A>G 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 0.463 in 389,296 control chromosomes in the GnomAD database, including 34,973 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 0.48 (14308 hom., cov: 31)
  • Exomes 𝑓: 0.45 (20665 hom.)
• Consequence: ENSG00000230563 ENST00000430097.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 5 publications found

Genes affected

ENSG00000230563 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430097.2. 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
	LOC643406	NR_029405.1		n.705A>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230563	ENST00000430097.2	TSL:1	n.694A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000230563	ENST00000651499.1		n.1053A>G		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000230563	ENST00000653367.1		n.730A>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.477 AC: 68761 AN: 144262 Hom.: 14300 Cov.: 31

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.523

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.480

GnomAD4 exome AF: 0.454 AC: 111265 AN: 244922 Hom.: 20665 Cov.: 0 AF XY: 0.453 AC XY: 62356 AN XY: 137776

African (AFR) AF: 0.527 AC: 3510 AN: 6656

American (AMR) AF: 0.493 AC: 9566 AN: 19392

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 3623 AN: 6504

East Asian (EAS) AF: 0.267 AC: 2359 AN: 8838

South Asian (SAS) AF: 0.454 AC: 21977 AN: 48422

European-Finnish (FIN) AF: 0.471 AC: 4795 AN: 10186

Middle Eastern (MID) AF: 0.488 AC: 519 AN: 1064

European-Non Finnish (NFE) AF: 0.450 AC: 59556 AN: 132256

Other (OTH) AF: 0.462 AC: 5360 AN: 11604

GnomAD4 genome AF: 0.477 AC: 68806 AN: 144374 Hom.: 14308 Cov.: 31 AF XY: 0.477 AC XY: 33614 AN XY: 70426

African (AFR) AF: 0.530 AC: 20905 AN: 39480

American (AMR) AF: 0.503 AC: 7246 AN: 14418

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 1917 AN: 3312

East Asian (EAS) AF: 0.270 AC: 1364 AN: 5058

South Asian (SAS) AF: 0.441 AC: 2003 AN: 4540

European-Finnish (FIN) AF: 0.477 AC: 4694 AN: 9840

Middle Eastern (MID) AF: 0.543 AC: 151 AN: 278

European-Non Finnish (NFE) AF: 0.454 AC: 29293 AN: 64568

Other (OTH) AF: 0.474 AC: 945 AN: 1994

Alfa AF: 0.476 Hom.: 1645

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.26
PhyloP100		-0.74

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: rs1060236;

hg19: chr20-5454686;

COSMIC: COSV107527291;