rs2206030

Variant names:

• chr6-35436577-T-C
• rs2206030

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 0.631 in 152,182 control chromosomes in the GnomAD database, including 32,572 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 0.63 (32572 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 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: 0.632 AC: 96044 AN: 152066 Hom.: 32546 Cov.: 34

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.608

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

GnomAD4 genome AF: 0.631 AC: 96097 AN: 152182 Hom.: 32572 Cov.: 34 AF XY: 0.633 AC XY: 47097 AN XY: 74400

Gnomad4 AFR AF: 0.384

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.432

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.754

Gnomad4 OTH AF: 0.610

Alfa AF: 0.702 Hom.: 4872

Bravo AF: 0.611

Asia WGS AF: 0.524 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.45
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2206030; hg19: chr6-35404354;