rs9378805

chr6-417727-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 0.368 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;