rs2143416

Variant names:

• chr1-186684633-A-C
• rs2143416

Your query was ambiguous. Multiple possible variants found:

• chr1-186684633-A-C
• chr1-186684633-A-T

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 0.267 in 151,910 control chromosomes in the GnomAD database, including 7,997 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 0.27 (7997 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.552 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: 0.267 AC: 40476 AN: 151794 Hom.: 7953 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0496

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.0867

Gnomad MID AF: 0.236

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.267 AC: 40578 AN: 151910 Hom.: 7997 Cov.: 32 AF XY: 0.260 AC XY: 19292 AN XY: 74264

Gnomad4 AFR AF: 0.558

Gnomad4 AMR AF: 0.203

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0493

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.0867

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.264

Alfa AF: 0.229 Hom.: 950

Bravo AF: 0.288

Asia WGS AF: 0.192 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.053
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2143416; hg19: chr1-186653765;