rs4645429

Variant names:

• chr6-95765839-A-G
• rs4645429

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0594 in 152,192 control chromosomes in the GnomAD database, including 394 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 0.059 (394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 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: 0.0594 AC: 9032 AN: 152076 Hom.: 391 Cov.: 32

Gnomad AFR AF: 0.0323

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0818

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0527

Gnomad OTH AF: 0.0546

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

GnomAD4 genome AF: 0.0594 AC: 9040 AN: 152192 Hom.: 394 Cov.: 32 AF XY: 0.0624 AC XY: 4644 AN XY: 74400

Gnomad4 AFR AF: 0.0323

Gnomad4 AMR AF: 0.0822

Gnomad4 ASJ AF: 0.0689

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0779

Gnomad4 NFE AF: 0.0528

Gnomad4 OTH AF: 0.0597

Alfa AF: 0.0535 Hom.: 42

Bravo AF: 0.0575

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	10
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4645429; hg19: chr6-96213715;