rs1385530

Variant names:

• chr6-79398248-T-C
• rs1385530

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 0.0844 in 152,192 control chromosomes in the GnomAD database, including 603 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 0.084 (603 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.119 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: 0.0845 AC: 12843 AN: 152074 Hom.: 603 Cov.: 31

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0907

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0844 AC: 12840 AN: 152192 Hom.: 603 Cov.: 31 AF XY: 0.0826 AC XY: 6146 AN XY: 74428

Gnomad4 AFR AF: 0.0412

Gnomad4 AMR AF: 0.0906

Gnomad4 ASJ AF: 0.164

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0520

Gnomad4 NFE AF: 0.106

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0984 Hom.: 122

Bravo AF: 0.0850

Asia WGS AF: 0.108 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
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: rs1385530; hg19: chr6-80107965;