6-49414480-G-A

Variant names:

• chr6-49414480-G-A
• rs9369898

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 0.589 in 150,244 control chromosomes in the GnomAD database, including 26,368 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 0.59 (26368 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 34 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.632 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: 0.589 AC: 88477 AN: 150148 Hom.: 26347 Cov.: 28

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.589 AC: 88533 AN: 150244 Hom.: 26368 Cov.: 28 AF XY: 0.584 AC XY: 42721 AN XY: 73202

African (AFR) AF: 0.593 AC: 24233 AN: 40838

American (AMR) AF: 0.436 AC: 6564 AN: 15038

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1955 AN: 3466

East Asian (EAS) AF: 0.462 AC: 2357 AN: 5104

South Asian (SAS) AF: 0.652 AC: 3100 AN: 4758

European-Finnish (FIN) AF: 0.604 AC: 6034 AN: 9986

Middle Eastern (MID) AF: 0.476 AC: 138 AN: 290

European-Non Finnish (NFE) AF: 0.626 AC: 42425 AN: 67782

Other (OTH) AF: 0.553 AC: 1149 AN: 2076

Alfa AF: 0.580 Hom.: 9462

Bravo AF: 0.568

Asia WGS AF: 0.548 AC: 1908 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	0.22
DANN	Benign	0.24
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9369898; hg19: chr6-49382193;