rs9307613

chr4-129436249-T-Achr4-129436249-T-C

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.514 in 151,970 control chromosomes in the GnomAD database, including 22,746 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 0.51 (22746 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.07

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.1).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77990 AN: 151852 Hom.: 22702 Cov.: 31

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.574

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.421

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.514 AC: 78096 AN: 151970 Hom.: 22746 Cov.: 31 AF XY: 0.511 AC XY: 37932 AN XY: 74268

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.400

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.421

Gnomad4 NFE AF: 0.397

Gnomad4 OTH AF: 0.512

Alfa AF: 0.313 Hom.: 796

Bravo AF: 0.524

Asia WGS AF: 0.523 AC: 1818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.10
Cadd	Benign	23
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9307613; hg19: chr4-130357404;