6-53001116-A-G

Position:

• chr6-53001116-A-G

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 0.197 in 152,042 control chromosomes in the GnomAD database, including 3,321 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 0.20 (3321 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29906 AN: 151924 Hom.: 3307 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0700

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.197 AC: 29940 AN: 152042 Hom.: 3321 Cov.: 32 AF XY: 0.191 AC XY: 14222 AN XY: 74340

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.0702

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.192

Alfa AF: 0.177 Hom.: 3337

Bravo AF: 0.205

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.74
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2397136; hg19: chr6-52865914;