2-211171950-T-C

Position:

• chr2-211171950-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 0.734 in 151,820 control chromosomes in the GnomAD database, including 41,186 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 0.73 (41186 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

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 = 0.807 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111319 AN: 151702 Hom.: 41162 Cov.: 31

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.734 AC: 111398 AN: 151820 Hom.: 41186 Cov.: 31 AF XY: 0.734 AC XY: 54415 AN XY: 74182

Gnomad4 AFR AF: 0.799

Gnomad4 AMR AF: 0.722

Gnomad4 ASJ AF: 0.652

Gnomad4 EAS AF: 0.828

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.723

Gnomad4 NFE AF: 0.702

Gnomad4 OTH AF: 0.724

Alfa AF: 0.722 Hom.: 6729

Bravo AF: 0.740

Asia WGS AF: 0.749 AC: 2600 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.19
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1437933; hg19: chr2-212036675;