2-143060149-T-C

Variant names:

• chr2-143060149-T-C
• rs354690

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 0.49 in 152,024 control chromosomes in the GnomAD database, including 18,969 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 0.49 (18969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.553 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: 0.490 AC: 74445 AN: 151906 Hom.: 18958 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.490 AC: 74491 AN: 152024 Hom.: 18969 Cov.: 32 AF XY: 0.486 AC XY: 36123 AN XY: 74318

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.585

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.291

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.558

Gnomad4 OTH AF: 0.515

Alfa AF: 0.546 Hom.: 47215

Bravo AF: 0.491

Asia WGS AF: 0.260 AC: 909 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs354690; hg19: chr2-143817718;