chr6-151632992-T-C

Variant names:

• chr6-151632992-T-C
• rs6900157

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 0.416 in 152,134 control chromosomes in the GnomAD database, including 15,301 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 0.42 (15301 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 28 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 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: 0.416 AC: 63183 AN: 152014 Hom.: 15278 Cov.: 33

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.416 AC: 63242 AN: 152134 Hom.: 15301 Cov.: 33 AF XY: 0.407 AC XY: 30279 AN XY: 74388

African (AFR) AF: 0.673 AC: 27898 AN: 41466

American (AMR) AF: 0.297 AC: 4536 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1176 AN: 3464

East Asian (EAS) AF: 0.346 AC: 1789 AN: 5176

South Asian (SAS) AF: 0.356 AC: 1715 AN: 4824

European-Finnish (FIN) AF: 0.194 AC: 2057 AN: 10606

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.335 AC: 22788 AN: 67988

Other (OTH) AF: 0.420 AC: 886 AN: 2110

Alfa AF: 0.352 Hom.: 17916

Bravo AF: 0.435

Asia WGS AF: 0.378 AC: 1311 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.7
DANN	Benign	0.57
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs6900157; hg19: chr6-151954127;