chr6-52185555-A-G

Variant names:

• chr6-52185555-A-G
• rs4711998

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 0.633 in 151,988 control chromosomes in the GnomAD database, including 32,251 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 0.63 (32251 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.739 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: 0.634 AC: 96234 AN: 151870 Hom.: 32237 Cov.: 30

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.633 AC: 96279 AN: 151988 Hom.: 32251 Cov.: 30 AF XY: 0.630 AC XY: 46797 AN XY: 74304

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.636

Alfa AF: 0.722 Hom.: 53359

Bravo AF: 0.628

Asia WGS AF: 0.441 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4711998; hg19: chr6-52050353;