rs1421379

Positions:

• chr6-46738257-G-A
• chr6-46738257-G-C

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 0.205 in 152,014 control chromosomes in the GnomAD database, including 3,569 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 0.21 (3569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31190 AN: 151896 Hom.: 3561 Cov.: 32

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.205 AC: 31221 AN: 152014 Hom.: 3569 Cov.: 32 AF XY: 0.213 AC XY: 15813 AN XY: 74314

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.221

Alfa AF: 0.198 Hom.: 5081

Bravo AF: 0.197

Asia WGS AF: 0.335 AC: 1162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1421379; hg19: chr6-46705994;