rs9378212

Positions:

• chr6-32477914-C-G
• chr6-32477914-C-T

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 0.104 in 128,482 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.10 (0 hom., cov: 36)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

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 = 0.146 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: 0.104 AC: 13320 AN: 128368 Hom.: 0 Cov.: 36

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.0405

Gnomad AMR AF: 0.0909

Gnomad ASJ AF: 0.0929

Gnomad EAS AF: 0.0727

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0910

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.104 AC: 13334 AN: 128482 Hom.: 0 Cov.: 36 AF XY: 0.104 AC XY: 6539 AN XY: 62998

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.0909

Gnomad4 ASJ AF: 0.0929

Gnomad4 EAS AF: 0.0725

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.0659

Gnomad4 NFE AF: 0.0910

Gnomad4 OTH AF: 0.109

Alfa AF: 0.0134 Hom.: 3574

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9378212; hg19: chr6-32445691;