rs1353387

Positions:

• chr4-81026030-G-A

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 0.666 in 152,116 control chromosomes in the GnomAD database, including 38,599 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 0.67 (38599 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.837 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: 0.667 AC: 101326 AN: 151998 Hom.: 38581 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.823

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.682

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.666 AC: 101356 AN: 152116 Hom.: 38599 Cov.: 32 AF XY: 0.668 AC XY: 49700 AN XY: 74356

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.682

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.793

Gnomad4 NFE AF: 0.843

Gnomad4 OTH AF: 0.688

Alfa AF: 0.748 Hom.: 5753

Bravo AF: 0.644

Asia WGS AF: 0.770 AC: 2676 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.67
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1353387; hg19: chr4-81947184;