rs2820211

Positions:

• chr1-238537407-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000442726.1(ENSG00000231877):​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: ENST00000442726.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.461

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124904565	XR_007066966.1	n.64+3895A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000442726.1	n.2002A>G		non_coding_transcript_exon_variant	4/4	2

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

Gnomad4 NFE exome AF: 0.438

Gnomad4 OTH exome AF: 0.00

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

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.452

Alfa AF: 0.441 Hom.: 20756

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2820211; hg19: chr1-238700707;