rs4742408

Variant names:

• chr9-7773723-C-A
• rs4742408

Your query was ambiguous. Multiple possible variants found:

• chr9-7773723-C-A
• chr9-7773723-C-G
• chr9-7773723-C-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 0.525 in 151,910 control chromosomes in the GnomAD database, including 24,507 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 0.53 (24507 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79780 AN: 151790 Hom.: 24509 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.783

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.525 AC: 79781 AN: 151910 Hom.: 24507 Cov.: 32 AF XY: 0.532 AC XY: 39530 AN XY: 74250

African (AFR) AF: 0.188 AC: 7807 AN: 41436

American (AMR) AF: 0.631 AC: 9631 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2121 AN: 3470

East Asian (EAS) AF: 0.898 AC: 4626 AN: 5154

South Asian (SAS) AF: 0.693 AC: 3333 AN: 4810

European-Finnish (FIN) AF: 0.639 AC: 6742 AN: 10556

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.640 AC: 43436 AN: 67916

Other (OTH) AF: 0.567 AC: 1198 AN: 2112

Alfa AF: 0.604 Hom.: 50119

Bravo AF: 0.514

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.39
DANN	Benign	0.54
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs4742408; hg19: chr9-7773723;