6-151642562-C-T

Variant names:

• chr6-151642562-C-T
• rs865898

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 0.609 in 152,008 control chromosomes in the GnomAD database, including 29,002 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 0.61 (29002 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.742 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: 0.608 AC: 92415 AN: 151890 Hom.: 28966 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.609 AC: 92501 AN: 152008 Hom.: 29002 Cov.: 32 AF XY: 0.602 AC XY: 44703 AN XY: 74286

African (AFR) AF: 0.749 AC: 31068 AN: 41482

American (AMR) AF: 0.475 AC: 7259 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2187 AN: 3466

East Asian (EAS) AF: 0.421 AC: 2172 AN: 5160

South Asian (SAS) AF: 0.586 AC: 2819 AN: 4810

European-Finnish (FIN) AF: 0.514 AC: 5414 AN: 10532

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.584 AC: 39676 AN: 67952

Other (OTH) AF: 0.600 AC: 1270 AN: 2116

Alfa AF: 0.574 Hom.: 14422

Bravo AF: 0.610

Asia WGS AF: 0.552 AC: 1923 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.77
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs865898; hg19: chr6-151963697;