chr6-92255579-T-C

Variant names:

• chr6-92255579-T-C
• rs1822589

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 0.21 in 152,046 control chromosomes in the GnomAD database, including 4,323 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 0.21 (4323 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31970 AN: 151928 Hom.: 4320 Cov.: 32

Gnomad AFR AF: 0.0534

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.210 AC: 31963 AN: 152046 Hom.: 4323 Cov.: 32 AF XY: 0.207 AC XY: 15359 AN XY: 74320

African (AFR) AF: 0.0533 AC: 2210 AN: 41496

American (AMR) AF: 0.178 AC: 2721 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1155 AN: 3472

East Asian (EAS) AF: 0.112 AC: 575 AN: 5154

South Asian (SAS) AF: 0.187 AC: 903 AN: 4822

European-Finnish (FIN) AF: 0.236 AC: 2495 AN: 10556

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21036 AN: 67954

Other (OTH) AF: 0.232 AC: 489 AN: 2110

Alfa AF: 0.246 Hom.: 8195

Bravo AF: 0.198

Asia WGS AF: 0.131 AC: 457 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	21
DANN	Benign	0.83
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1822589; hg19: chr6-92965297;