rs1444062

Positions:

• chr6-48486422-G-A
• chr6-48486422-G-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;