rs1398359

Variant names:

• chr5-19384985-G-A
• rs1398359

Your query was ambiguous. Multiple possible variants found:

• chr5-19384985-G-A
• chr5-19384985-G-C
• chr5-19384985-G-T

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 0.932 in 150,132 control chromosomes in the GnomAD database, including 65,953 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 0.93 (65953 hom., cov: 25)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.93
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 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: 0.932 AC: 139811 AN: 150030 Hom.: 65932 Cov.: 25

Gnomad AFR AF: 0.762

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.979

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.971

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.940

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

GnomAD4 genome AF: 0.932 AC: 139885 AN: 150132 Hom.: 65953 Cov.: 25 AF XY: 0.934 AC XY: 68284 AN XY: 73114

African (AFR) AF: 0.762 AC: 31007 AN: 40710

American (AMR) AF: 0.979 AC: 14665 AN: 14986

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3466 AN: 3466

East Asian (EAS) AF: 1.00 AC: 5003 AN: 5004

South Asian (SAS) AF: 0.999 AC: 4783 AN: 4788

European-Finnish (FIN) AF: 1.00 AC: 9982 AN: 9982

Middle Eastern (MID) AF: 0.969 AC: 281 AN: 290

European-Non Finnish (NFE) AF: 0.999 AC: 67816 AN: 67900

Other (OTH) AF: 0.941 AC: 1970 AN: 2094

Alfa AF: 0.944 Hom.: 4926

Bravo AF: 0.922

Asia WGS AF: 0.985 AC: 3427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.27
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs1398359; hg19: chr5-19385094;