chr6-153945865-C-T

Variant names:

• chr6-153945865-C-T
• rs9397674

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 0.236 in 152,056 control chromosomes in the GnomAD database, including 4,546 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 0.24 (4546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35812 AN: 151938 Hom.: 4535 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.236 AC: 35828 AN: 152056 Hom.: 4546 Cov.: 32 AF XY: 0.244 AC XY: 18165 AN XY: 74334

African (AFR) AF: 0.177 AC: 7348 AN: 41490

American (AMR) AF: 0.398 AC: 6079 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 927 AN: 3468

East Asian (EAS) AF: 0.327 AC: 1691 AN: 5164

South Asian (SAS) AF: 0.391 AC: 1885 AN: 4818

European-Finnish (FIN) AF: 0.243 AC: 2575 AN: 10576

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14454 AN: 67956

Other (OTH) AF: 0.267 AC: 563 AN: 2106

Alfa AF: 0.213 Hom.: 556

Bravo AF: 0.239

Asia WGS AF: 0.377 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.52
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9397674; hg19: chr6-154267000;