6-155608667-C-T

Variant names:

• chr6-155608667-C-T
• rs35229355

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 0.0468 in 151,950 control chromosomes in the GnomAD database, including 520 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 0.047 (520 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.360
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 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: 0.0468 AC: 7100 AN: 151832 Hom.: 522 Cov.: 33

Gnomad AFR AF: 0.0696

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0291

Gnomad ASJ AF: 0.0205

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.00389

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0155

Gnomad OTH AF: 0.0475

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

GnomAD4 genome AF: 0.0468 AC: 7108 AN: 151950 Hom.: 520 Cov.: 33 AF XY: 0.0495 AC XY: 3674 AN XY: 74256

African (AFR) AF: 0.0696 AC: 2881 AN: 41414

American (AMR) AF: 0.0290 AC: 443 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0205 AC: 71 AN: 3468

East Asian (EAS) AF: 0.376 AC: 1941 AN: 5158

South Asian (SAS) AF: 0.102 AC: 490 AN: 4814

European-Finnish (FIN) AF: 0.00389 AC: 41 AN: 10540

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0155 AC: 1056 AN: 67974

Other (OTH) AF: 0.0517 AC: 109 AN: 2108

Alfa AF: 0.0412 Hom.: 822

Bravo AF: 0.0516

Asia WGS AF: 0.231 AC: 802 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.0
DANN	Benign	0.34
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs35229355; hg19: chr6-155929801;