rs1755038

Variant names:

• chr6-33497642-G-A
• rs1755038

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;