2-226235138-T-C

Position:

• chr2-226235138-T-C

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.226235138T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;