2-143932550-C-T

Variant names:

• chr2-143932550-C-T
• rs1011397

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 0.773 in 152,170 control chromosomes in the GnomAD database, including 46,658 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 0.77 (46658 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.947
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.839 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: 0.773 AC: 117557 AN: 152052 Hom.: 46633 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.796

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

GnomAD4 genome AF: 0.773 AC: 117629 AN: 152170 Hom.: 46658 Cov.: 32 AF XY: 0.780 AC XY: 58047 AN XY: 74406

African (AFR) AF: 0.584 AC: 24200 AN: 41466

American (AMR) AF: 0.820 AC: 12535 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2825 AN: 3468

East Asian (EAS) AF: 0.805 AC: 4172 AN: 5184

South Asian (SAS) AF: 0.780 AC: 3762 AN: 4820

European-Finnish (FIN) AF: 0.939 AC: 9958 AN: 10608

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57423 AN: 68012

Other (OTH) AF: 0.794 AC: 1680 AN: 2116

Alfa AF: 0.805 Hom.: 120004

Bravo AF: 0.753

Asia WGS AF: 0.795 AC: 2762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.53
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs1011397; hg19: chr2-144690117;