rs9478495

Variant names:

• chr6-154002774-G-A
• rs9478495

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 0.188 in 152,166 control chromosomes in the GnomAD database, including 2,910 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 0.19 (2910 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.348
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.242 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: 0.188 AC: 28647 AN: 152048 Hom.: 2903 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0539

Gnomad SAS AF: 0.0708

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.188 AC: 28681 AN: 152166 Hom.: 2910 Cov.: 32 AF XY: 0.186 AC XY: 13857 AN XY: 74382

African (AFR) AF: 0.222 AC: 9203 AN: 41514

American (AMR) AF: 0.249 AC: 3804 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3470

East Asian (EAS) AF: 0.0544 AC: 282 AN: 5184

South Asian (SAS) AF: 0.0711 AC: 343 AN: 4824

European-Finnish (FIN) AF: 0.212 AC: 2240 AN: 10572

Middle Eastern (MID) AF: 0.158 AC: 46 AN: 292

European-Non Finnish (NFE) AF: 0.169 AC: 11494 AN: 67992

Other (OTH) AF: 0.189 AC: 398 AN: 2110

Alfa AF: 0.173 Hom.: 9909

Bravo AF: 0.195

Asia WGS AF: 0.0750 AC: 261 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.8
DANN	Benign	0.11
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs9478495; hg19: chr6-154323909;