chr6-48813874-A-G

Variant names:

• chr6-48813874-A-G
• rs1938206

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.739

Gnomad4 AMR AF: 0.887

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.838

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.882

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.832

Alfa AF: 0.830 Hom.: 6144

Bravo AF: 0.820

Asia WGS AF: 0.835 AC: 2902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1938206; hg19: chr6-48781511;