rs5743305

Positions:

• chr4-186068179-T-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 0.349 in 152,064 control chromosomes in the GnomAD database, including 9,452 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 0.35 (9452 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53027 AN: 151944 Hom.: 9444 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.536

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.371

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

GnomAD4 genome AF: 0.349 AC: 53066 AN: 152064 Hom.: 9452 Cov.: 32 AF XY: 0.346 AC XY: 25728 AN XY: 74318

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.536

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.378

Gnomad4 OTH AF: 0.371

Alfa AF: 0.362 Hom.: 1488

Bravo AF: 0.348

Asia WGS AF: 0.346 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5743305; hg19: chr4-186989333;