chr2-120544335-C-T

Variant names:

• chr2-120544335-C-T
• rs6721654
• ENST00000651018.1:n.544G>A

Variant summary

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

The ENST00000651018.1(ENSG00000237614):​n.544G>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 0.143 in 152,144 control chromosomes in the GnomAD database, including 2,297 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 0.14 (2296 hom., cov: 33)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: ENSG00000237614 ENST00000651018.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 11 publications found

Genes affected

ENSG00000237614 (HGNC:):

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 = 0.277 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651018.1. 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
	ENSG00000237614	ENST00000651018.1		n.544G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000237614	ENST00000655876.1		n.915G>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000303222	ENST00000792896.1		n.599C>T		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21707 AN: 151998 Hom.: 2296 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0893

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.120

GnomAD4 exome AF: 0.115 AC: 3 AN: 26 Hom.: 1 Cov.: 0 AF XY: 0.143 AC XY: 2 AN XY: 14

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.100 AC: 2 AN: 20

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.143 AC: 21726 AN: 152118 Hom.: 2296 Cov.: 33 AF XY: 0.143 AC XY: 10627 AN XY: 74364

African (AFR) AF: 0.281 AC: 11663 AN: 41436

American (AMR) AF: 0.0892 AC: 1364 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3470

East Asian (EAS) AF: 0.210 AC: 1086 AN: 5176

South Asian (SAS) AF: 0.202 AC: 975 AN: 4824

European-Finnish (FIN) AF: 0.0833 AC: 883 AN: 10600

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0766 AC: 5206 AN: 67998

Other (OTH) AF: 0.119 AC: 252 AN: 2112

Alfa AF: 0.107 Hom.: 1837

Bravo AF: 0.145

Asia WGS AF: 0.232 AC: 807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.6
DANN	Benign	0.68
PhyloP100		0.069

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: rs6721654;

hg19: chr2-121301911;