chr6-52222236-T-G

Variant names:

• chr6-52222236-T-G
• rs11966760

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 0.272 in 152,138 control chromosomes in the GnomAD database, including 7,125 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 0.27 (7125 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 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: 0.272 AC: 41348 AN: 152020 Hom.: 7126 Cov.: 32

Gnomad AFR AF: 0.0672

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.272 AC: 41341 AN: 152138 Hom.: 7125 Cov.: 32 AF XY: 0.278 AC XY: 20689 AN XY: 74386

African (AFR) AF: 0.0671 AC: 2786 AN: 41526

American (AMR) AF: 0.234 AC: 3581 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2351 AN: 5172

South Asian (SAS) AF: 0.394 AC: 1900 AN: 4818

European-Finnish (FIN) AF: 0.458 AC: 4843 AN: 10566

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24036 AN: 67980

Other (OTH) AF: 0.280 AC: 591 AN: 2114

Alfa AF: 0.282 Hom.: 2224

Bravo AF: 0.243

Asia WGS AF: 0.361 AC: 1258 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.9
DANN	Benign	0.59
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs11966760; hg19: chr6-52087034;