rs9405675

Variant names:

• chr6-444600-G-A
• rs9405675

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 0.515 in 152,130 control chromosomes in the GnomAD database, including 22,323 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 0.51 (22323 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 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: 0.515 AC: 78271 AN: 152010 Hom.: 22315 Cov.: 33

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.515 AC: 78309 AN: 152130 Hom.: 22323 Cov.: 33 AF XY: 0.512 AC XY: 38121 AN XY: 74386

African (AFR) AF: 0.267 AC: 11068 AN: 41500

American (AMR) AF: 0.569 AC: 8700 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.688 AC: 2385 AN: 3468

East Asian (EAS) AF: 0.352 AC: 1819 AN: 5170

South Asian (SAS) AF: 0.466 AC: 2248 AN: 4824

European-Finnish (FIN) AF: 0.649 AC: 6868 AN: 10578

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43243 AN: 67986

Other (OTH) AF: 0.561 AC: 1185 AN: 2112

Alfa AF: 0.589 Hom.: 73931

Bravo AF: 0.499

Asia WGS AF: 0.398 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.60
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs9405675; hg19: chr6-444600;