chr6-6016936-A-G

Variant names:

• chr6-6016936-A-G
• rs1475157

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 0.17 in 152,064 control chromosomes in the GnomAD database, including 2,313 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 0.17 (2313 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.204 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: 0.170 AC: 25855 AN: 151946 Hom.: 2312 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.181

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.170 AC: 25865 AN: 152064 Hom.: 2313 Cov.: 32 AF XY: 0.167 AC XY: 12398 AN XY: 74356

African (AFR) AF: 0.154 AC: 6397 AN: 41460

American (AMR) AF: 0.168 AC: 2564 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.245 AC: 851 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1113 AN: 5184

South Asian (SAS) AF: 0.136 AC: 655 AN: 4820

European-Finnish (FIN) AF: 0.128 AC: 1356 AN: 10582

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.181 AC: 12329 AN: 67952

Other (OTH) AF: 0.159 AC: 336 AN: 2112

Alfa AF: 0.181 Hom.: 6824

Bravo AF: 0.175

Asia WGS AF: 0.162 AC: 566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.4
DANN	Benign	0.64
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1475157; hg19: chr6-6017169;