6-41414834-A-G

Variant names:

• chr6-41414834-A-G
• rs9357360

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 0.764 in 152,116 control chromosomes in the GnomAD database, including 44,682 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 0.76 (44682 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 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: 0.764 AC: 116157 AN: 151998 Hom.: 44644 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.702

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.764 AC: 116253 AN: 152116 Hom.: 44682 Cov.: 32 AF XY: 0.769 AC XY: 57141 AN XY: 74348

African (AFR) AF: 0.679 AC: 28175 AN: 41472

American (AMR) AF: 0.787 AC: 12025 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 2438 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4583 AN: 5166

South Asian (SAS) AF: 0.874 AC: 4212 AN: 4820

European-Finnish (FIN) AF: 0.824 AC: 8726 AN: 10584

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53784 AN: 68000

Other (OTH) AF: 0.727 AC: 1535 AN: 2110

Alfa AF: 0.779 Hom.: 179309

Bravo AF: 0.755

Asia WGS AF: 0.875 AC: 3043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs9357360; hg19: chr6-41382572;