rs5743305

Variant names:

• chr4-186068179-T-A
• rs5743305

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 0.349 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
• Publications: 72 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.300 AC: 12461 AN: 41468

American (AMR) AF: 0.329 AC: 5025 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.536 AC: 1859 AN: 3470

East Asian (EAS) AF: 0.268 AC: 1387 AN: 5166

South Asian (SAS) AF: 0.412 AC: 1986 AN: 4816

European-Finnish (FIN) AF: 0.320 AC: 3387 AN: 10570

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

European-Non Finnish (NFE) AF: 0.378 AC: 25706 AN: 67966

Other (OTH) AF: 0.371 AC: 785 AN: 2116

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs5743305; hg19: chr4-186989333;