chr6-20533152-G-T

Variant names:

• chr6-20533152-G-T
• rs9368197

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 0.243 in 151,662 control chromosomes in the GnomAD database, including 5,465 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 0.24 (5465 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.150
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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: 0.243 AC: 36816 AN: 151544 Hom.: 5463 Cov.: 29

Gnomad AFR AF: 0.0786

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.243 AC: 36817 AN: 151662 Hom.: 5465 Cov.: 29 AF XY: 0.251 AC XY: 18580 AN XY: 74080

African (AFR) AF: 0.0784 AC: 3246 AN: 41424

American (AMR) AF: 0.336 AC: 5114 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1042 AN: 3466

East Asian (EAS) AF: 0.529 AC: 2718 AN: 5136

South Asian (SAS) AF: 0.423 AC: 2032 AN: 4806

European-Finnish (FIN) AF: 0.297 AC: 3102 AN: 10456

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18640 AN: 67870

Other (OTH) AF: 0.260 AC: 547 AN: 2104

Alfa AF: 0.270 Hom.: 9159

Bravo AF: 0.237

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.4
DANN	Benign	0.64
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9368197; hg19: chr6-20533383;