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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373585	XR_001739681.3	n.4554G>A		non_coding_transcript_exon_variant	Exon 4 of 4
LOC105373585	XR_002959417.2	n.2467G>A		non_coding_transcript_exon_variant	Exon 3 of 4
LOC105373585	XR_007087217.1	n.3923G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LOC105373585	XR_007087218.1	n.2559G>A		non_coding_transcript_exon_variant	Exon 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000237614	ENST00000651018.1	n.544G>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000237614	ENST00000655876.1	n.915G>A		non_coding_transcript_exon_variant	Exon 1 of 2
ENSG00000303222	ENST00000792896.1	n.599C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000237614	ENST00000413991.1	n.-9G>A		upstream_gene_variant		3

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 v4.3

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

Other links and lift over

dbSNP: rs6721654; hg19: chr2-121301911;