5-135236539-A-G

Variant names:

• chr5-135236539-A-G
• rs606854
• ENST00000505663.1:n.1857T>C

Variant summary

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

The ENST00000505663.1(LINC02900):​n.1857T>C 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 0.689 in 151,894 control chromosomes in the GnomAD database, including 36,314 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 0.69 (36247 hom., cov: 29)
  • Exomes 𝑓: 0.74 (67 hom.)
• Consequence: LINC02900 ENST00000505663.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 6 publications found

Genes affected

LINC02900 (HGNC:27964): (long intergenic non-protein coding RNA 2900)

PITX1-AS1 (HGNC:48332): (PITX1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.749 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505663.1. 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
	LINC02900	NR_037895.1		n.1855T>C		non_coding_transcript_exon	Exon 4 of 4
	PITX1-AS1	NR_161235.1		n.467+62367A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02900	ENST00000505663.1	TSL:1	n.1857T>C		non_coding_transcript_exon	Exon 4 of 4
	PITX1-AS1	ENST00000513931.2	TSL:3	n.341-59956A>G		intron	N/A
	PITX1-AS1	ENST00000624272.3	TSL:2	n.461+62367A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.689 AC: 104396 AN: 151538 Hom.: 36219 Cov.: 29

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.817

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.669

GnomAD4 exome AF: 0.735 AC: 175 AN: 238 Hom.: 67 Cov.: 0 AF XY: 0.735 AC XY: 100 AN XY: 136

African (AFR) AF: 0.875 AC: 7 AN: 8

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 3 AN: 4

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AF: 0.750 AC: 3 AN: 4

European-Finnish (FIN) AF: 0.733 AC: 85 AN: 116

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.714 AC: 70 AN: 98

Other (OTH) AF: 0.833 AC: 5 AN: 6

GnomAD4 genome AF: 0.689 AC: 104473 AN: 151656 Hom.: 36247 Cov.: 29 AF XY: 0.688 AC XY: 50981 AN XY: 74072

African (AFR) AF: 0.756 AC: 31205 AN: 41276

American (AMR) AF: 0.680 AC: 10384 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2050 AN: 3470

East Asian (EAS) AF: 0.674 AC: 3447 AN: 5116

South Asian (SAS) AF: 0.661 AC: 3160 AN: 4782

European-Finnish (FIN) AF: 0.691 AC: 7264 AN: 10508

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.657 AC: 44622 AN: 67916

Other (OTH) AF: 0.669 AC: 1412 AN: 2112

Alfa AF: 0.651 Hom.: 22657

Bravo AF: 0.727

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.33
PhyloP100		-0.096

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: rs606854;

hg19: chr5-134572229;