rs9291256

chr4-44939348-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 0.0616 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;