rs9455973

Variant names:

• chr6-168182326-G-A
• rs9455973

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 0.217 in 152,112 control chromosomes in the GnomAD database, including 5,709 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 0.22 (5709 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.77
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 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: 0.217 AC: 32965 AN: 151994 Hom.: 5687 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.0280

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0915

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.217 AC: 33031 AN: 152112 Hom.: 5709 Cov.: 33 AF XY: 0.217 AC XY: 16141 AN XY: 74394

African (AFR) AF: 0.468 AC: 19391 AN: 41458

American (AMR) AF: 0.204 AC: 3121 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 443 AN: 3472

East Asian (EAS) AF: 0.348 AC: 1795 AN: 5156

South Asian (SAS) AF: 0.260 AC: 1250 AN: 4814

European-Finnish (FIN) AF: 0.0280 AC: 297 AN: 10606

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.0915 AC: 6221 AN: 67996

Other (OTH) AF: 0.213 AC: 449 AN: 2112

Alfa AF: 0.137 Hom.: 3817

Bravo AF: 0.238

Asia WGS AF: 0.301 AC: 1048 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.32
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs9455973; hg19: chr6-168583006;