chr6-153951229-A-G

Variant names:

• chr6-153951229-A-G
• rs610040

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 0.799 in 152,148 control chromosomes in the GnomAD database, including 48,963 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 (48963 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.288
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.88 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121525 AN: 152030 Hom.: 48937 Cov.: 31

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.839

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.791

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.799 AC: 121599 AN: 152148 Hom.: 48963 Cov.: 31 AF XY: 0.802 AC XY: 59636 AN XY: 74372

African (AFR) AF: 0.888 AC: 36868 AN: 41526

American (AMR) AF: 0.832 AC: 12729 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2330 AN: 3472

East Asian (EAS) AF: 0.756 AC: 3918 AN: 5180

South Asian (SAS) AF: 0.788 AC: 3798 AN: 4818

European-Finnish (FIN) AF: 0.824 AC: 8706 AN: 10568

Middle Eastern (MID) AF: 0.668 AC: 195 AN: 292

European-Non Finnish (NFE) AF: 0.745 AC: 50643 AN: 67972

Other (OTH) AF: 0.778 AC: 1647 AN: 2116

Alfa AF: 0.761 Hom.: 5930

Bravo AF: 0.804

Asia WGS AF: 0.756 AC: 2628 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.75
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs610040; hg19: chr6-154272364;