rs9291256

Variant names:

• chr4-44939348-G-T
• rs9291256

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 0.0616 in 151,650 control chromosomes in the GnomAD database, including 350 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 0.062 (350 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0803 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: 0.0617 AC: 9349 AN: 151532 Hom.: 350 Cov.: 32

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0894

Gnomad EAS AF: 0.00273

Gnomad SAS AF: 0.0614

Gnomad FIN AF: 0.0864

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.0490

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

GnomAD4 genome AF: 0.0616 AC: 9341 AN: 151650 Hom.: 350 Cov.: 32 AF XY: 0.0604 AC XY: 4473 AN XY: 74078

Gnomad4 AFR AF: 0.0343

Gnomad4 AMR AF: 0.0409

Gnomad4 ASJ AF: 0.0894

Gnomad4 EAS AF: 0.00254

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.0864

Gnomad4 NFE AF: 0.0821

Gnomad4 OTH AF: 0.0485

Alfa AF: 0.0680 Hom.: 64

Bravo AF: 0.0568

Asia WGS AF: 0.0320 AC: 115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.35
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9291256; hg19: chr4-44941365;