rs9312159

Positions:

• chr4-66557148-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.169 in 152,188 control chromosomes in the GnomAD database, including 4,073 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 0.17 (4073 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25718 AN: 152070 Hom.: 4051 Cov.: 33

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.0569

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0424

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.169 AC: 25784 AN: 152188 Hom.: 4073 Cov.: 33 AF XY: 0.167 AC XY: 12413 AN XY: 74414

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.0569

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0420

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0714

Gnomad4 OTH AF: 0.145

Alfa AF: 0.135 Hom.: 338

Bravo AF: 0.179

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.26
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9312159; hg19: chr4-67422866;