6-48813874-A-G

Variant names:

• chr6-48813874-A-G
• rs1938206

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 0.821 in 152,124 control chromosomes in the GnomAD database, including 51,560 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 0.82 (51560 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.875 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: 0.821 AC: 124820 AN: 152006 Hom.: 51520 Cov.: 32

Gnomad AFR AF: 0.739

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.838

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.821 AC: 124918 AN: 152124 Hom.: 51560 Cov.: 32 AF XY: 0.826 AC XY: 61375 AN XY: 74338

African (AFR) AF: 0.739 AC: 30655 AN: 41484

American (AMR) AF: 0.887 AC: 13543 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.897 AC: 3115 AN: 3472

East Asian (EAS) AF: 0.838 AC: 4330 AN: 5164

South Asian (SAS) AF: 0.804 AC: 3876 AN: 4820

European-Finnish (FIN) AF: 0.882 AC: 9344 AN: 10592

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57363 AN: 68008

Other (OTH) AF: 0.832 AC: 1758 AN: 2114

Alfa AF: 0.827 Hom.: 6366

Bravo AF: 0.820

Asia WGS AF: 0.835 AC: 2902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1938206; hg19: chr6-48781511;