rs9378805

Variant names:

• chr6-417727-A-C
• rs9378805

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 47 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.107 AC: 4429 AN: 41536

American (AMR) AF: 0.446 AC: 6825 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2007 AN: 3470

East Asian (EAS) AF: 0.309 AC: 1597 AN: 5170

South Asian (SAS) AF: 0.419 AC: 2019 AN: 4814

European-Finnish (FIN) AF: 0.463 AC: 4904 AN: 10584

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.483 AC: 32807 AN: 67964

Other (OTH) AF: 0.400 AC: 845 AN: 2112

Alfa AF: 0.444 Hom.: 58100

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
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs9378805; hg19: chr6-417727;