chr2-202032645-C-T

Variant names:

• chr2-202032645-C-T
• rs2280509
• ENST00000608741.2:n.893G>A

Variant summary

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

The ENST00000608741.2(ENSG00000273209):​n.893G>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 0.145 in 152,216 control chromosomes in the GnomAD database, including 2,070 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 (2067 hom., cov: 32)
  • Exomes 𝑓: 0.26 (3 hom.)
• Consequence: ENSG00000273209 ENST00000608741.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.798
• Publications: 7 publications found

Genes affected

ENSG00000273209 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.333 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000273209	ENST00000608741.2	n.893G>A		non_coding_transcript_exon_variant	Exon 1 of 2	6
ENSG00000289026	ENST00000691022.2	n.596C>T		non_coding_transcript_exon_variant	Exon 1 of 1
ENSG00000289026	ENST00000738740.1	n.184C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22070 AN: 152034 Hom.: 2073 Cov.: 32

Gnomad AFR AF: 0.0458

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.158

GnomAD4 exome AF: 0.258 AC: 16 AN: 62 Hom.: 3 AF XY: 0.273 AC XY: 12 AN XY: 44

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

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.208 AC: 10 AN: 48

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.145 AC: 22059 AN: 152154 Hom.: 2067 Cov.: 32 AF XY: 0.146 AC XY: 10889 AN XY: 74374

African (AFR) AF: 0.0458 AC: 1901 AN: 41542

American (AMR) AF: 0.150 AC: 2296 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 388 AN: 3472

East Asian (EAS) AF: 0.257 AC: 1325 AN: 5160

South Asian (SAS) AF: 0.347 AC: 1669 AN: 4814

European-Finnish (FIN) AF: 0.137 AC: 1452 AN: 10580

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12289 AN: 67974

Other (OTH) AF: 0.159 AC: 335 AN: 2112

Alfa AF: 0.146 Hom.: 256

Bravo AF: 0.141

Asia WGS AF: 0.320 AC: 1113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.6
DANN	Benign	0.78
PhyloP100		-0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2280509; hg19: chr2-202897368;