rs9450278

Variant names:

• chr6-85448624-G-A
• rs9450278

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 0.192 in 152,146 control chromosomes in the GnomAD database, including 3,377 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 (3377 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.324 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: 0.192 AC: 29123 AN: 152028 Hom.: 3376 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.0625

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.192 AC: 29149 AN: 152146 Hom.: 3377 Cov.: 33 AF XY: 0.186 AC XY: 13856 AN XY: 74368

African (AFR) AF: 0.328 AC: 13624 AN: 41476

American (AMR) AF: 0.134 AC: 2050 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3466

East Asian (EAS) AF: 0.0624 AC: 323 AN: 5174

South Asian (SAS) AF: 0.168 AC: 807 AN: 4810

European-Finnish (FIN) AF: 0.106 AC: 1124 AN: 10598

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.149 AC: 10119 AN: 68016

Other (OTH) AF: 0.170 AC: 359 AN: 2110

Alfa AF: 0.171 Hom.: 3847

Bravo AF: 0.198

Asia WGS AF: 0.117 AC: 408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.91
DANN	Benign	0.56
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs9450278; hg19: chr6-86158342;