rs9378805

Variant names:

• chr6-417727-A-C
• rs9378805

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 0.368 in 152,140 control chromosomes in the GnomAD database, including 12,389 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 0.37 (12389 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

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 (NFE) allele frequency at 95% confidence interval = 0.478 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: 0.368 AC: 55936 AN: 152022 Hom.: 12390 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.368 AC: 55940 AN: 152140 Hom.: 12389 Cov.: 32 AF XY: 0.367 AC XY: 27276 AN XY: 74370

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.400

Alfa AF: 0.467 Hom.: 39618

Bravo AF: 0.357

Asia WGS AF: 0.348 AC: 1209 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	0.33
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9378805; hg19: chr6-417727;