rs9472236

Variant names:

• chr6-44239013-G-A
• rs9472236

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 0.153 in 152,146 control chromosomes in the GnomAD database, including 2,315 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 0.15 (2315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.35 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: 0.153 AC: 23234 AN: 152028 Hom.: 2315 Cov.: 32

Gnomad AFR AF: 0.0439

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.153 AC: 23232 AN: 152146 Hom.: 2315 Cov.: 32 AF XY: 0.157 AC XY: 11668 AN XY: 74374

African (AFR) AF: 0.0437 AC: 1815 AN: 41508

American (AMR) AF: 0.240 AC: 3666 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 460 AN: 3470

East Asian (EAS) AF: 0.364 AC: 1883 AN: 5178

South Asian (SAS) AF: 0.289 AC: 1393 AN: 4822

European-Finnish (FIN) AF: 0.183 AC: 1932 AN: 10580

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.170 AC: 11540 AN: 68002

Other (OTH) AF: 0.152 AC: 320 AN: 2112

Alfa AF: 0.174 Hom.: 4456

Bravo AF: 0.154

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	8.2
DANN	Benign	0.77
PhyloP100		-0.014

Splicing

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

Other links and lift over

dbSNP: rs9472236; hg19: chr6-44206750;