rs386618

Positions:

• chr6-160313432-T-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 0.462 in 151,786 control chromosomes in the GnomAD database, including 16,676 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 0.46 (16676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.462 AC: 70103 AN: 151666 Hom.: 16663 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.533

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.462 AC: 70165 AN: 151786 Hom.: 16676 Cov.: 32 AF XY: 0.462 AC XY: 34291 AN XY: 74182

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.430

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.411

Gnomad4 FIN AF: 0.527

Gnomad4 NFE AF: 0.533

Gnomad4 OTH AF: 0.486

Alfa AF: 0.512 Hom.: 4662

Bravo AF: 0.457

Asia WGS AF: 0.351 AC: 1220 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.3
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs386618; hg19: chr6-160734464;