rs2972149

Positions:

• chr2-226227434-T-A

Variant summary

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

The variant allele was found at a frequency of 0.455 in 152,144 control chromosomes in the GnomAD database, including 16,062 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 0.46 (16062 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.226227434T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.455 AC: 69207 AN: 152026 Hom.: 16045 Cov.: 33

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.538

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.483

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.455 AC: 69252 AN: 152144 Hom.: 16062 Cov.: 33 AF XY: 0.452 AC XY: 33586 AN XY: 74366

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.538

Gnomad4 ASJ AF: 0.574

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.490

Alfa AF: 0.471 Hom.: 2122

Bravo AF: 0.462

Asia WGS AF: 0.581 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	4.4
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2972149; hg19: chr2-227092150;