chr6-48486422-G-A

Variant names:

• chr6-48486422-G-A
• rs1444062

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 0.536 in 151,926 control chromosomes in the GnomAD database, including 22,808 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 0.54 (22808 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.67 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: 0.536 AC: 81370 AN: 151808 Hom.: 22783 Cov.: 33

Gnomad AFR AF: 0.677

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.505

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.536 AC: 81441 AN: 151926 Hom.: 22808 Cov.: 33 AF XY: 0.536 AC XY: 39770 AN XY: 74242

Gnomad4 AFR AF: 0.677

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.465

Gnomad4 EAS AF: 0.209

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.505

Gnomad4 OTH AF: 0.493

Alfa AF: 0.424 Hom.: 1256

Bravo AF: 0.529

Asia WGS AF: 0.390 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.53
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1444062; hg19: chr6-48454158;