rs1353387

Variant names:

• chr4-81026030-G-A
• rs1353387

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 0.666 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
• Publications: 4 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.263 AC: 10929 AN: 41478

American (AMR) AF: 0.773 AC: 11810 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.682 AC: 2365 AN: 3470

East Asian (EAS) AF: 0.808 AC: 4173 AN: 5164

South Asian (SAS) AF: 0.820 AC: 3949 AN: 4814

European-Finnish (FIN) AF: 0.793 AC: 8400 AN: 10594

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.843 AC: 57313 AN: 67992

Other (OTH) AF: 0.688 AC: 1455 AN: 2114

Alfa AF: 0.729 Hom.: 5787

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
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs1353387; hg19: chr4-81947184;