6-93004087-T-C

Variant names:

• chr6-93004087-T-C
• rs652520

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 0.58 in 151,918 control chromosomes in the GnomAD database, including 26,984 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 0.58 (26984 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.711
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.78 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: 0.580 AC: 88003 AN: 151800 Hom.: 26946 Cov.: 31

Gnomad AFR AF: 0.787

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.580 AC: 88091 AN: 151918 Hom.: 26984 Cov.: 31 AF XY: 0.577 AC XY: 42864 AN XY: 74240

African (AFR) AF: 0.788 AC: 32634 AN: 41438

American (AMR) AF: 0.541 AC: 8259 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1990 AN: 3468

East Asian (EAS) AF: 0.649 AC: 3351 AN: 5160

South Asian (SAS) AF: 0.564 AC: 2715 AN: 4818

European-Finnish (FIN) AF: 0.441 AC: 4645 AN: 10538

Middle Eastern (MID) AF: 0.647 AC: 189 AN: 292

European-Non Finnish (NFE) AF: 0.482 AC: 32706 AN: 67920

Other (OTH) AF: 0.552 AC: 1164 AN: 2110

Alfa AF: 0.514 Hom.: 89365

Bravo AF: 0.597

Asia WGS AF: 0.604 AC: 2099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
DANN	Benign	0.46
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs652520; hg19: chr6-93713805;