rs6583654

Variant names:

• chr8-141802904-T-C
• rs6583654

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 0.434 in 152,096 control chromosomes in the GnomAD database, including 14,808 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 0.43 (14808 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.461 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: 0.434 AC: 65899 AN: 151976 Hom.: 14762 Cov.: 33

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.0453

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.434 AC: 66008 AN: 152096 Hom.: 14808 Cov.: 33 AF XY: 0.429 AC XY: 31891 AN XY: 74348

African (AFR) AF: 0.445 AC: 18468 AN: 41496

American (AMR) AF: 0.470 AC: 7183 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1389 AN: 3464

East Asian (EAS) AF: 0.0452 AC: 234 AN: 5176

South Asian (SAS) AF: 0.421 AC: 2028 AN: 4822

European-Finnish (FIN) AF: 0.372 AC: 3928 AN: 10572

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.461 AC: 31360 AN: 67974

Other (OTH) AF: 0.424 AC: 896 AN: 2112

Alfa AF: 0.449 Hom.: 19531

Bravo AF: 0.440

Asia WGS AF: 0.293 AC: 1022 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.27
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs6583654; hg19: chr8-142884265;