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. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.141 AC: 5830 AN: 41472

American (AMR) AF: 0.289 AC: 4407 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 980 AN: 3468

East Asian (EAS) AF: 0.168 AC: 867 AN: 5170

South Asian (SAS) AF: 0.471 AC: 2263 AN: 4808

European-Finnish (FIN) AF: 0.227 AC: 2399 AN: 10552

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.202 AC: 13756 AN: 67972

Other (OTH) AF: 0.221 AC: 466 AN: 2110

Alfa AF: 0.199 Hom.: 8633

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
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1421379; hg19: chr6-46705994;