chr6-89323223-T-C

Variant names:

• chr6-89323223-T-C
• rs2064831

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 0.152 in 152,154 control chromosomes in the GnomAD database, including 2,027 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 0.15 (2027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.251 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: 0.152 AC: 23072 AN: 152036 Hom.: 2028 Cov.: 32

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.169

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.152 AC: 23079 AN: 152154 Hom.: 2027 Cov.: 32 AF XY: 0.156 AC XY: 11587 AN XY: 74372

African (AFR) AF: 0.0664 AC: 2757 AN: 41538

American (AMR) AF: 0.183 AC: 2789 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3472

East Asian (EAS) AF: 0.189 AC: 981 AN: 5184

South Asian (SAS) AF: 0.263 AC: 1266 AN: 4816

European-Finnish (FIN) AF: 0.169 AC: 1785 AN: 10582

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

European-Non Finnish (NFE) AF: 0.177 AC: 12000 AN: 67974

Other (OTH) AF: 0.176 AC: 371 AN: 2108

Alfa AF: 0.173 Hom.: 1286

Bravo AF: 0.146

Asia WGS AF: 0.230 AC: 798 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	0.098
DANN	Benign	0.52
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs2064831; hg19: chr6-90032942;