6-84848744-G-A

Position:

• chr6-84848744-G-A

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 0.371 in 152,056 control chromosomes in the GnomAD database, including 12,200 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 0.37 (12200 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.57 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: 0.371 AC: 56367 AN: 151938 Hom.: 12196 Cov.: 33

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.371 AC: 56390 AN: 152056 Hom.: 12200 Cov.: 33 AF XY: 0.374 AC XY: 27761 AN XY: 74298

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.522

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.402

Alfa AF: 0.443 Hom.: 7722

Bravo AF: 0.346

Asia WGS AF: 0.483 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	12
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2324753; hg19: chr6-85558462;