rs1755038

chr6-33497642-G-A

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 0.907 in 152,254 control chromosomes in the GnomAD database, including 62,747 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 0.91 (62747 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.907 AC: 138046 AN: 152136 Hom.: 62696 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.985

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.926

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.906

Gnomad OTH AF: 0.917

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

GnomAD4 genome AF: 0.907 AC: 138152 AN: 152254 Hom.: 62747 Cov.: 32 AF XY: 0.911 AC XY: 67788 AN XY: 74446

Gnomad4 AFR AF: 0.881

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.985

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.980

Gnomad4 FIN AF: 0.926

Gnomad4 NFE AF: 0.906

Gnomad4 OTH AF: 0.918

Alfa AF: 0.911 Hom.: 7838

Bravo AF: 0.903

Asia WGS AF: 0.963 AC: 3350 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	1.4
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1755038; hg19: chr6-33465419;