6-92878264-A-T

Variant names:

• chr6-92878264-A-T
• rs1591741

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 0.444 in 151,582 control chromosomes in the GnomAD database, including 16,631 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 0.44 (16631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 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: 0.445 AC: 67343 AN: 151468 Hom.: 16641 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.455

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.444 AC: 67347 AN: 151582 Hom.: 16631 Cov.: 32 AF XY: 0.441 AC XY: 32685 AN XY: 74050

African (AFR) AF: 0.248 AC: 10260 AN: 41378

American (AMR) AF: 0.505 AC: 7698 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3470

East Asian (EAS) AF: 0.897 AC: 4616 AN: 5148

South Asian (SAS) AF: 0.503 AC: 2414 AN: 4802

European-Finnish (FIN) AF: 0.402 AC: 4192 AN: 10438

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34368 AN: 67804

Other (OTH) AF: 0.471 AC: 991 AN: 2106

Alfa AF: 0.220 Hom.: 430

Bravo AF: 0.447

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.20
DANN	Benign	0.80
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1591741; hg19: chr6-93587982;