rs1364893

Variant names:

• chr4-59838624-A-T
• rs1364893

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 0.503 in 151,772 control chromosomes in the GnomAD database, including 19,515 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 0.50 (19515 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.624
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.583 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: 0.503 AC: 76275 AN: 151654 Hom.: 19504 Cov.: 33

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.503 AC: 76298 AN: 151772 Hom.: 19515 Cov.: 33 AF XY: 0.499 AC XY: 37031 AN XY: 74164

African (AFR) AF: 0.481 AC: 19909 AN: 41418

American (AMR) AF: 0.593 AC: 9019 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1680 AN: 3468

East Asian (EAS) AF: 0.302 AC: 1553 AN: 5138

South Asian (SAS) AF: 0.355 AC: 1713 AN: 4826

European-Finnish (FIN) AF: 0.505 AC: 5324 AN: 10552

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.521 AC: 35322 AN: 67852

Other (OTH) AF: 0.490 AC: 1034 AN: 2112

Alfa AF: 0.516 Hom.: 2528

Bravo AF: 0.513

Asia WGS AF: 0.282 AC: 986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.3
DANN	Benign	0.72
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs1364893; hg19: chr4-60704342;