rs9391227

Variant names:

• chr6-104710759-T-A
• rs9391227

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 0.55 in 152,086 control chromosomes in the GnomAD database, including 24,457 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 0.55 (24457 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.759 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: 0.550 AC: 83568 AN: 151968 Hom.: 24428 Cov.: 32

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.550 AC: 83640 AN: 152086 Hom.: 24457 Cov.: 32 AF XY: 0.549 AC XY: 40810 AN XY: 74350

African (AFR) AF: 0.766 AC: 31809 AN: 41514

American (AMR) AF: 0.541 AC: 8253 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2272 AN: 5168

South Asian (SAS) AF: 0.469 AC: 2261 AN: 4820

European-Finnish (FIN) AF: 0.476 AC: 5030 AN: 10572

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31039 AN: 67970

Other (OTH) AF: 0.508 AC: 1071 AN: 2110

Alfa AF: 0.507 Hom.: 2547

Bravo AF: 0.568

Asia WGS AF: 0.421 AC: 1469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.3
DANN	Benign	0.79
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs9391227; hg19: chr6-105158634; COSMIC: COSV60262451;