rs1325474

Variant names:

• chr6-83829706-G-A
• rs1325474

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 0.241 in 152,068 control chromosomes in the GnomAD database, including 7,759 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 0.24 (7759 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 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: 0.240 AC: 36476 AN: 151950 Hom.: 7718 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.0781

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.0692

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0807

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.241 AC: 36583 AN: 152068 Hom.: 7759 Cov.: 32 AF XY: 0.239 AC XY: 17811 AN XY: 74370

Gnomad4 AFR AF: 0.559

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.0781

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.0692

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.0807

Gnomad4 OTH AF: 0.195

Alfa AF: 0.180 Hom.: 583

Bravo AF: 0.271

Asia WGS AF: 0.175 AC: 610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1325474; hg19: chr6-84539425;