rs1421379

Variant names:

• chr6-46738257-G-A
• rs1421379

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;