chr6-84255564-T-C

Variant names:

• chr6-84255564-T-C
• rs1324089

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 0.779 in 152,164 control chromosomes in the GnomAD database, including 46,280 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 0.78 (46280 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 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: 0.779 AC: 118417 AN: 152046 Hom.: 46226 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.769

Gnomad OTH AF: 0.749

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

GnomAD4 genome AF: 0.779 AC: 118530 AN: 152164 Hom.: 46280 Cov.: 33 AF XY: 0.777 AC XY: 57803 AN XY: 74376

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.774

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.769

Gnomad4 OTH AF: 0.750

Alfa AF: 0.770 Hom.: 86603

Bravo AF: 0.783

Asia WGS AF: 0.718 AC: 2492 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.030
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1324089; hg19: chr6-84965282;