6-89235807-C-T

Variant names:

• chr6-89235807-C-T
• rs9342188

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 0.932 in 152,306 control chromosomes in the GnomAD database, including 66,263 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 0.93 (66263 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.908
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.932 AC: 141800 AN: 152188 Hom.: 66199 Cov.: 33

Gnomad AFR AF: 0.983

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.941

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.976

Gnomad FIN AF: 0.879

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.936

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

GnomAD4 genome AF: 0.932 AC: 141924 AN: 152306 Hom.: 66263 Cov.: 33 AF XY: 0.933 AC XY: 69523 AN XY: 74480

African (AFR) AF: 0.983 AC: 40861 AN: 41582

American (AMR) AF: 0.941 AC: 14402 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3108 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5187 AN: 5190

South Asian (SAS) AF: 0.977 AC: 4721 AN: 4832

European-Finnish (FIN) AF: 0.879 AC: 9312 AN: 10592

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61316 AN: 68014

Other (OTH) AF: 0.937 AC: 1981 AN: 2114

Alfa AF: 0.923 Hom.: 8042

Bravo AF: 0.937

Asia WGS AF: 0.986 AC: 3431 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	1.0
DANN	Benign	0.31
PhyloP100		-0.91

Splicing

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

Other links and lift over

dbSNP: rs9342188; hg19: chr6-89945526;