2-226235138-T-C

Variant names:

• chr2-226235138-T-C
• rs2972147

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 0.672 in 152,052 control chromosomes in the GnomAD database, including 34,509 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 0.67 (34509 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.905 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: 0.672 AC: 102025 AN: 151934 Hom.: 34474 Cov.: 31

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.712

Gnomad EAS AF: 0.926

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.638

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.672 AC: 102110 AN: 152052 Hom.: 34509 Cov.: 31 AF XY: 0.673 AC XY: 50032 AN XY: 74314

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.712

Gnomad4 EAS AF: 0.927

Gnomad4 SAS AF: 0.769

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.638

Gnomad4 OTH AF: 0.666

Alfa AF: 0.664 Hom.: 6503

Bravo AF: 0.681

Asia WGS AF: 0.847 AC: 2944 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.23
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2972147; hg19: chr2-227099854;