chr6-16127176-C-T

Variant names:

• chr6-16127176-C-T
• rs3757354

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 0.274 in 151,976 control chromosomes in the GnomAD database, including 6,097 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 0.27 (6097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 102 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.384 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: 0.274 AC: 41549 AN: 151858 Hom.: 6076 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.397

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.274 AC: 41629 AN: 151976 Hom.: 6097 Cov.: 32 AF XY: 0.277 AC XY: 20602 AN XY: 74278

African (AFR) AF: 0.352 AC: 14569 AN: 41424

American (AMR) AF: 0.309 AC: 4713 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 763 AN: 3462

East Asian (EAS) AF: 0.398 AC: 2057 AN: 5168

South Asian (SAS) AF: 0.308 AC: 1481 AN: 4804

European-Finnish (FIN) AF: 0.248 AC: 2617 AN: 10560

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14772 AN: 67970

Other (OTH) AF: 0.233 AC: 492 AN: 2108

Alfa AF: 0.239 Hom.: 14527

Bravo AF: 0.279

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.2
DANN	Benign	0.76
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs3757354; hg19: chr6-16127407;