6-52185988-A-G

Position:

• chr6-52185988-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BA1

The variant allele was found at a frequency of 0.343 in 152,016 control chromosomes in the GnomAD database, including 9,284 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency: Genomes: 𝑓 0.34 (9284 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 6-52185988-A-G is Benign according to our data. Variant chr6-52185988-A-G is described in Lovd as [Benign].
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52183 AN: 151898 Hom.: 9283 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.343 AC: 52192 AN: 152016 Hom.: 9284 Cov.: 32 AF XY: 0.346 AC XY: 25707 AN XY: 74294

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.382

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.369

Gnomad4 OTH AF: 0.345

Alfa AF: 0.342 Hom.: 9389

Bravo AF: 0.324

Asia WGS AF: 0.392 AC: 1366 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3819024; hg19: chr6-52050786;