chr6-45755251-T-C

Variant names:

• chr6-45755251-T-C
• rs321329

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 0.634 in 152,006 control chromosomes in the GnomAD database, including 31,286 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 0.63 (31286 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 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: 0.634 AC: 96302 AN: 151888 Hom.: 31245 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.634 AC: 96396 AN: 152006 Hom.: 31286 Cov.: 31 AF XY: 0.637 AC XY: 47308 AN XY: 74300

African (AFR) AF: 0.780 AC: 32327 AN: 41454

American (AMR) AF: 0.598 AC: 9145 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.619 AC: 2149 AN: 3470

East Asian (EAS) AF: 0.468 AC: 2414 AN: 5158

South Asian (SAS) AF: 0.733 AC: 3529 AN: 4812

European-Finnish (FIN) AF: 0.619 AC: 6538 AN: 10564

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.565 AC: 38358 AN: 67946

Other (OTH) AF: 0.623 AC: 1315 AN: 2112

Alfa AF: 0.586 Hom.: 111613

Bravo AF: 0.639

Asia WGS AF: 0.590 AC: 2052 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.53
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs321329; hg19: chr6-45722988;