rs9312159

Variant names:

• chr4-66557148-G-T
• rs9312159

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 0.169 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.416 AC: 17262 AN: 41504

American (AMR) AF: 0.107 AC: 1639 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0569 AC: 197 AN: 3464

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5180

South Asian (SAS) AF: 0.0420 AC: 203 AN: 4832

European-Finnish (FIN) AF: 0.116 AC: 1225 AN: 10584

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0714 AC: 4854 AN: 68010

Other (OTH) AF: 0.145 AC: 306 AN: 2114

Alfa AF: 0.145 Hom.: 401

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
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs9312159; hg19: chr4-67422866;