rs213212

Positions:

• chr6-33218141-C-A
• chr6-33218141-C-G
• chr6-33218141-C-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 0.782 in 151,716 control chromosomes in the GnomAD database, including 46,792 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 0.78 (46792 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.525

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118477 AN: 151598 Hom.: 46743 Cov.: 29

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.984

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.782 AC: 118582 AN: 151716 Hom.: 46792 Cov.: 29 AF XY: 0.783 AC XY: 58085 AN XY: 74142

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.796

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.908

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.800

Alfa AF: 0.742 Hom.: 54882

Bravo AF: 0.791

Asia WGS AF: 0.908 AC: 3157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs213212; hg19: chr6-33185918;