6-48126403-G-A

Variant names:

• chr6-48126403-G-A
• rs7739016

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 0.185 in 151,996 control chromosomes in the GnomAD database, including 2,978 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 0.19 (2978 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 1 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 = 0.283 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28118 AN: 151878 Hom.: 2972 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.185 AC: 28151 AN: 151996 Hom.: 2978 Cov.: 32 AF XY: 0.187 AC XY: 13868 AN XY: 74298

African (AFR) AF: 0.287 AC: 11900 AN: 41432

American (AMR) AF: 0.218 AC: 3330 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 700 AN: 3468

East Asian (EAS) AF: 0.164 AC: 850 AN: 5170

South Asian (SAS) AF: 0.155 AC: 746 AN: 4820

European-Finnish (FIN) AF: 0.124 AC: 1313 AN: 10576

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8782 AN: 67944

Other (OTH) AF: 0.183 AC: 387 AN: 2112

Alfa AF: 0.162 Hom.: 1224

Bravo AF: 0.196

Asia WGS AF: 0.175 AC: 609 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	2.8
DANN	Benign	0.61
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7739016; hg19: chr6-48094139;