rs2972149

Variant names:

• chr2-226227434-T-A
• rs2972149

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.756
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.367 AC: 15226 AN: 41516

American (AMR) AF: 0.538 AC: 8231 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1989 AN: 3466

East Asian (EAS) AF: 0.479 AC: 2477 AN: 5176

South Asian (SAS) AF: 0.518 AC: 2497 AN: 4820

European-Finnish (FIN) AF: 0.398 AC: 4213 AN: 10580

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33087 AN: 67978

Other (OTH) AF: 0.490 AC: 1033 AN: 2110

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
PhyloP100		0.76

Splicing

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

Other links and lift over

dbSNP: rs2972149; hg19: chr2-227092150;