chr6-84848744-G-A

Variant names:

• chr6-84848744-G-A
• rs2324753

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 0.371 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
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.150 AC: 6243 AN: 41486

American (AMR) AF: 0.327 AC: 5000 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1809 AN: 3468

East Asian (EAS) AF: 0.428 AC: 2215 AN: 5172

South Asian (SAS) AF: 0.588 AC: 2830 AN: 4810

European-Finnish (FIN) AF: 0.473 AC: 4985 AN: 10548

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31842 AN: 67980

Other (OTH) AF: 0.402 AC: 850 AN: 2112

Alfa AF: 0.441 Hom.: 8519

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
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs2324753; hg19: chr6-85558462;