6-24158909-G-A

Variant names:

• chr6-24158909-G-A
• rs7754552

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 0.89 in 152,046 control chromosomes in the GnomAD database, including 60,994 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 0.89 (60994 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.890 AC: 135266 AN: 151928 Hom.: 60955 Cov.: 30

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.929

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.961

Gnomad FIN AF: 0.986

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.949

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.890 AC: 135363 AN: 152046 Hom.: 60994 Cov.: 30 AF XY: 0.894 AC XY: 66454 AN XY: 74358

African (AFR) AF: 0.728 AC: 30123 AN: 41364

American (AMR) AF: 0.929 AC: 14196 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.927 AC: 3214 AN: 3468

East Asian (EAS) AF: 0.997 AC: 5162 AN: 5178

South Asian (SAS) AF: 0.961 AC: 4629 AN: 4818

European-Finnish (FIN) AF: 0.986 AC: 10450 AN: 10600

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.949 AC: 64578 AN: 68014

Other (OTH) AF: 0.907 AC: 1918 AN: 2114

Alfa AF: 0.909 Hom.: 7728

Bravo AF: 0.876

Asia WGS AF: 0.956 AC: 3325 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.27
DANN	Benign	0.30
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs7754552; hg19: chr6-24159137;