6-153957178-G-A

Variant names:

• chr6-153957178-G-A
• rs613030

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 0.8 in 152,150 control chromosomes in the GnomAD database, including 49,015 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 0.80 (49015 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.882 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.800 AC: 121577 AN: 152032 Hom.: 48989 Cov.: 32

Gnomad AFR AF: 0.890

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.790

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.672

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.800 AC: 121651 AN: 152150 Hom.: 49015 Cov.: 32 AF XY: 0.802 AC XY: 59650 AN XY: 74354

African (AFR) AF: 0.889 AC: 36942 AN: 41540

American (AMR) AF: 0.833 AC: 12729 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2329 AN: 3470

East Asian (EAS) AF: 0.756 AC: 3906 AN: 5166

South Asian (SAS) AF: 0.788 AC: 3788 AN: 4808

European-Finnish (FIN) AF: 0.823 AC: 8702 AN: 10574

Middle Eastern (MID) AF: 0.671 AC: 196 AN: 292

European-Non Finnish (NFE) AF: 0.745 AC: 50649 AN: 67990

Other (OTH) AF: 0.779 AC: 1645 AN: 2112

Alfa AF: 0.771 Hom.: 5892

Bravo AF: 0.805

Asia WGS AF: 0.757 AC: 2632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.34
DANN	Benign	0.42
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs613030; hg19: chr6-154278313;