rs213220

Variant names:

• chr6-33234863-C-T
• rs213220

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.584 in 151,872 control chromosomes in the GnomAD database, including 26,512 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 0.58 (26512 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 25 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.753 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: 0.584 AC: 88643 AN: 151754 Hom.: 26493 Cov.: 30

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.773

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.713

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.584 AC: 88701 AN: 151872 Hom.: 26512 Cov.: 30 AF XY: 0.581 AC XY: 43087 AN XY: 74176

African (AFR) AF: 0.667 AC: 27633 AN: 41398

American (AMR) AF: 0.550 AC: 8384 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2450 AN: 3468

East Asian (EAS) AF: 0.773 AC: 3978 AN: 5148

South Asian (SAS) AF: 0.623 AC: 3001 AN: 4816

European-Finnish (FIN) AF: 0.488 AC: 5146 AN: 10540

Middle Eastern (MID) AF: 0.719 AC: 210 AN: 292

European-Non Finnish (NFE) AF: 0.531 AC: 36080 AN: 67938

Other (OTH) AF: 0.652 AC: 1377 AN: 2112

Alfa AF: 0.555 Hom.: 54959

Bravo AF: 0.594

Asia WGS AF: 0.716 AC: 2489 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	1.5
DANN	Benign	0.87
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs213220; hg19: chr6-33202640;