rs6477450

Variant names:

• chr9-105677156-A-T
• rs6477450

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 0.524 in 152,088 control chromosomes in the GnomAD database, including 23,803 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 0.52 (23803 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.806 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: 0.523 AC: 79524 AN: 151970 Hom.: 23756 Cov.: 32

Gnomad AFR AF: 0.813

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.524 AC: 79625 AN: 152088 Hom.: 23803 Cov.: 32 AF XY: 0.521 AC XY: 38716 AN XY: 74348

African (AFR) AF: 0.813 AC: 33747 AN: 41498

American (AMR) AF: 0.497 AC: 7597 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1833 AN: 3468

East Asian (EAS) AF: 0.626 AC: 3229 AN: 5160

South Asian (SAS) AF: 0.425 AC: 2046 AN: 4814

European-Finnish (FIN) AF: 0.354 AC: 3746 AN: 10576

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25754 AN: 67972

Other (OTH) AF: 0.538 AC: 1136 AN: 2110

Alfa AF: 0.458 Hom.: 2311

Bravo AF: 0.551

Asia WGS AF: 0.530 AC: 1842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.1
DANN	Benign	0.70
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs6477450; hg19: chr9-108439437;