6-212006-T-C

Variant names:

• chr6-212006-T-C
• rs6596835

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 0.425 in 152,116 control chromosomes in the GnomAD database, including 16,531 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 0.43 (16531 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 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: 0.425 AC: 64572 AN: 151998 Hom.: 16499 Cov.: 33

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.425 AC: 64666 AN: 152116 Hom.: 16531 Cov.: 33 AF XY: 0.424 AC XY: 31499 AN XY: 74340

African (AFR) AF: 0.712 AC: 29545 AN: 41470

American (AMR) AF: 0.368 AC: 5625 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1279 AN: 3470

East Asian (EAS) AF: 0.649 AC: 3365 AN: 5182

South Asian (SAS) AF: 0.308 AC: 1487 AN: 4822

European-Finnish (FIN) AF: 0.275 AC: 2912 AN: 10576

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19282 AN: 67978

Other (OTH) AF: 0.416 AC: 880 AN: 2114

Alfa AF: 0.264 Hom.: 3138

Bravo AF: 0.444

Asia WGS AF: 0.515 AC: 1788 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.35
DANN	Benign	0.34
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs6596835; hg19: chr6-212006;