rs5014418

Positions:

• chr6-32751604-A-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 0.117 in 152,042 control chromosomes in the GnomAD database, including 1,665 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 0.12 (1665 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

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 (AFR) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17733 AN: 151924 Hom.: 1663 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.0782

Gnomad EAS AF: 0.00557

Gnomad SAS AF: 0.0151

Gnomad FIN AF: 0.00530

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0675

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.117 AC: 17741 AN: 152042 Hom.: 1665 Cov.: 32 AF XY: 0.112 AC XY: 8336 AN XY: 74348

Gnomad4 AFR AF: 0.250

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.0782

Gnomad4 EAS AF: 0.00539

Gnomad4 SAS AF: 0.0151

Gnomad4 FIN AF: 0.00530

Gnomad4 NFE AF: 0.0676

Gnomad4 OTH AF: 0.148

Alfa AF: 0.0886 Hom.: 193

Bravo AF: 0.138

Asia WGS AF: 0.0210 AC: 72 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	3.2
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5014418; hg19: chr6-32719381;