rs2820211

Variant names:

• chr1-238537407-A-G
• rs2820211
• ENST00000442726.1:n.2002A>G

Variant summary

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

The ENST00000442726.1(ENSG00000234464):​n.2002A>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 0.439 in 151,972 control chromosomes in the GnomAD database, including 14,863 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 0.44 (14861 hom., cov: 32)
  • Exomes 𝑓: 0.39 (2 hom.)
• Consequence: ENSG00000234464 ENST00000442726.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461
• Publications: 3 publications found

Genes affected

ENSG00000234464 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124904565	XR_007066966.1	n.64+3895A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000234464	ENST00000442726.1	n.2002A>G		non_coding_transcript_exon_variant	Exon 4 of 4	2
ENSG00000234464	ENST00000716151.1	n.547+38117A>G		intron_variant	Intron 5 of 7
ENSG00000234464	ENST00000716155.1	n.472+1610A>G		intron_variant	Intron 5 of 8

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66665 AN: 151834 Hom.: 14848 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.448

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.456

GnomAD4 exome AF: 0.389 AC: 7 AN: 18 Hom.: 2 Cov.: 0 AF XY: 0.357 AC XY: 5 AN XY: 14

African (AFR) AC: 0 AN: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.438 AC: 7 AN: 16

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

GnomAD4 genome AF: 0.439 AC: 66703 AN: 151954 Hom.: 14861 Cov.: 32 AF XY: 0.435 AC XY: 32277 AN XY: 74266

African (AFR) AF: 0.487 AC: 20195 AN: 41434

American (AMR) AF: 0.376 AC: 5738 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1548 AN: 3470

East Asian (EAS) AF: 0.368 AC: 1897 AN: 5150

South Asian (SAS) AF: 0.389 AC: 1871 AN: 4812

European-Finnish (FIN) AF: 0.392 AC: 4135 AN: 10552

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29852 AN: 67952

Other (OTH) AF: 0.452 AC: 954 AN: 2112

Alfa AF: 0.440 Hom.: 30657

Bravo AF: 0.438

Asia WGS AF: 0.408 AC: 1424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.83
DANN	Benign	0.53
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs2820211; hg19: chr1-238700707;