6-48706980-G-A

Variant names:

• chr6-48706980-G-A
• rs10484857

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 0.122 in 151,698 control chromosomes in the GnomAD database, including 1,394 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 0.12 (1394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.207 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: 0.122 AC: 18545 AN: 151584 Hom.: 1392 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0934

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.0818

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.0849

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.122 AC: 18557 AN: 151698 Hom.: 1394 Cov.: 32 AF XY: 0.124 AC XY: 9223 AN XY: 74162

African (AFR) AF: 0.211 AC: 8727 AN: 41392

American (AMR) AF: 0.0932 AC: 1421 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0525 AC: 182 AN: 3464

East Asian (EAS) AF: 0.0819 AC: 424 AN: 5174

South Asian (SAS) AF: 0.158 AC: 760 AN: 4814

European-Finnish (FIN) AF: 0.0921 AC: 971 AN: 10544

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.0850 AC: 5758 AN: 67752

Other (OTH) AF: 0.119 AC: 251 AN: 2106

Alfa AF: 0.0979 Hom.: 3124

Bravo AF: 0.125

Asia WGS AF: 0.109 AC: 378 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.7
DANN	Benign	0.83
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10484857; hg19: chr6-48674613;