rs2143079

Variant names:

• chr6-50816275-C-G
• rs2143079

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0343 in 152,274 control chromosomes in the GnomAD database, including 143 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 0.034 (143 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.45

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0562 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: 0.0343 AC: 5224 AN: 152156 Hom.: 143 Cov.: 33

Gnomad AFR AF: 0.00910

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0121

Gnomad ASJ AF: 0.0236

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0122

Gnomad FIN AF: 0.0468

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0577

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0343 AC: 5224 AN: 152274 Hom.: 143 Cov.: 33 AF XY: 0.0327 AC XY: 2433 AN XY: 74458

Gnomad4 AFR AF: 0.00910

Gnomad4 AMR AF: 0.0121

Gnomad4 ASJ AF: 0.0236

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.0468

Gnomad4 NFE AF: 0.0577

Gnomad4 OTH AF: 0.0222

Alfa AF: 0.0483 Hom.: 22

Bravo AF: 0.0308

Asia WGS AF: 0.00808 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
CADD	Benign	21
DANN	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2143079; hg19: chr6-50783988;