rs4742409

Variant names:

• chr9-7774180-A-C
• rs4742409

Your query was ambiguous. Multiple possible variants found:

• chr9-7774180-A-C
• chr9-7774180-A-G
• chr9-7774180-A-T

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 0.611 in 152,012 control chromosomes in the GnomAD database, including 30,004 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 0.61 (30004 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.88 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: 0.611 AC: 92807 AN: 151894 Hom.: 29999 Cov.: 32

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.901

Gnomad SAS AF: 0.715

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.611 AC: 92837 AN: 152012 Hom.: 30004 Cov.: 32 AF XY: 0.614 AC XY: 45644 AN XY: 74312

African (AFR) AF: 0.381 AC: 15783 AN: 41432

American (AMR) AF: 0.683 AC: 10414 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2346 AN: 3472

East Asian (EAS) AF: 0.902 AC: 4662 AN: 5170

South Asian (SAS) AF: 0.715 AC: 3453 AN: 4832

European-Finnish (FIN) AF: 0.661 AC: 6987 AN: 10564

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.690 AC: 46884 AN: 67974

Other (OTH) AF: 0.644 AC: 1357 AN: 2108

Alfa AF: 0.669 Hom.: 67653

Bravo AF: 0.606

Asia WGS AF: 0.733 AC: 2547 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.9
DANN	Benign	0.89
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs4742409; hg19: chr9-7774180;