6-41414489-C-G

Variant names:

• chr6-41414489-C-G
• rs1853406

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 0.765 in 152,056 control chromosomes in the GnomAD database, including 44,714 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 (44714 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.228
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.867 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: 0.765 AC: 116172 AN: 151938 Hom.: 44674 Cov.: 31

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.787

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.874

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.765 AC: 116270 AN: 152056 Hom.: 44714 Cov.: 31 AF XY: 0.769 AC XY: 57178 AN XY: 74352

African (AFR) AF: 0.680 AC: 28173 AN: 41446

American (AMR) AF: 0.787 AC: 12025 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2437 AN: 3468

East Asian (EAS) AF: 0.888 AC: 4580 AN: 5156

South Asian (SAS) AF: 0.876 AC: 4220 AN: 4816

European-Finnish (FIN) AF: 0.824 AC: 8731 AN: 10596

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

European-Non Finnish (NFE) AF: 0.791 AC: 53794 AN: 67978

Other (OTH) AF: 0.727 AC: 1535 AN: 2112

Alfa AF: 0.777 Hom.: 5724

Bravo AF: 0.755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.8
DANN	Benign	0.74
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs1853406; hg19: chr6-41382227;