rs4520040

Variant names:

• chr6-103984290-G-A
• rs4520040

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 0.0869 in 151,976 control chromosomes in the GnomAD database, including 938 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 0.087 (938 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 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: 0.0866 AC: 13144 AN: 151858 Hom.: 926 Cov.: 31

Gnomad AFR AF: 0.0970

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0219

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0438

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0869 AC: 13201 AN: 151976 Hom.: 938 Cov.: 31 AF XY: 0.0926 AC XY: 6878 AN XY: 74272

Gnomad4 AFR AF: 0.0976

Gnomad4 AMR AF: 0.157

Gnomad4 ASJ AF: 0.0219

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.0765

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0438

Gnomad4 OTH AF: 0.0841

Alfa AF: 0.0621 Hom.: 933

Bravo AF: 0.0923

Asia WGS AF: 0.173 AC: 600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4520040; hg19: chr6-104432165;